The issue of men receiving longer prison sentences is pretty well known, but I figured I would post a collection of studies I've found on the issue (many of these I ran across on MRA subs).

Given the same evidence, men are more likely to be found guilty, and are given harsher punishments. They are also more likely to be suspected, accused, and arrested to begin with, even when innocent. In one study, this effect was as high as 48%, depending on the type of crime. Meaning if a man and a woman both commit the same crime, a man is up to 48% more likely to be suspected and charged with that crime. This happens before the bias in court shows up, making it a cumulative effect.

Causes

The problem goes much deeper than just a sentencing disparity. Police profiling, harassment, negative male stereotypes, and other forms of social disadvantage, likely play a role. Examples of social disadvantages include things like hiring discrimination, discrimination in the education system, unemployment, homelessness, increased pressure to be "successful", a lack of resources for male victims of domestic violence, and a lack of research into men's mental health. Men's mental health in particular has been neglected in favor of women's mental health (or for a "one size fits all" solution which inadvertantly focuses on women). This is in part because many mental health problems were once thought to primarily effect women. The problem is that men who suffer from those problems are more likely to be incarcerated, instead of helped or treated. Which then causes them to not show up in some of those statistics.

Criminality is often seen as a reflection of the failures of society, instead of the individual. So if men make up a majority of the criminals in a society, that demonstrates an underlying form of disadvantage suffered by men. Put simply, men commit more crime because they are more likely to be put into situations where criminality becomes a rational option.

The prison disparity is therefore as much of an issue on its own as it is a symptom of other issues that effect men.

Gender and race

Another interesting topic is the intersection between gender and race. As alluded to above, men are seen as more dangerous and more prone to criminality. Which is also an issue that effects minorities, and minority men in particular.

Some people have noticed the racial trend and argued that mass incarceration is a form of institutionalized discrimination against minorities, and possibly even a modern form of legalized slavery. Even though the racial element gets highlighted, people are not so quick to admit that the same thing applies to gender. And that is despite gender being a much larger factor than race (statistically speaking).

Of course the point of saying this isn't to diminish the problem of racism in society. It is instead meant to point out one of the ways that men's rights issues are treated unfairly in comparison to issues that effect other groups. For example, if the situation was reversed, and effected women instead of men, we would be doing everything in our power to fix the problem. But because men are effected, it largely gets ignored. In fact, some people want to reduce the number of women in prison already, even though it effects men more (instead of fixing it for everyone, or focusing on the unique problems that men face, they focus on the group that already has it the best). This is a pattern that you find quite frequently for men's issues. And that pattern is itself, I would argue, a men's issue in it's own right.

The fact that we acknowledge this problem when it effects racial minorities (and even women), but not men, even when it effects men to a much higher degree, speaks volumes about how men's issues are treated by society.

Sources

Men are significantly more likely to be arrested for the same crime
Stolzenberg, L., & D'Alessio, S. J. (2004). Sex differences in the likelihood of arrest. Journal of Criminal Justice, 32(5), 443-454. [PDF] Available from: https://www.researchgate.net/profile/Lisa_Stolzenberg/publication/4970699_Sex_Differences_in_the_Likelihood_of_Arrest./links/004635333805a867e1000000.pdf
Men are more likely to be found guilty in court trials given the same evidence and mitigating circumstances
Hedderman, C., & Gelsthorpe, L. (Eds.). (1997). Understanding the sentencing of women. London: Home Office. Full Book: http://webarchive.nationalarchives.gov.uk/20110314171826/http://rds.homeoffice.gov.uk/rds/pdfs/hors170.pdf
Women receive a broad pass when it comes to sexual assault, especially sexual assault against young children, which distorts federal reporting and statistics on the topic
Denov, M. S. (2003). The myth of innocence: Sexual scripts and the recognition of child sexual abuse by female perpetrators. Journal of Sex Research, 40(3), 303-314. Available from: https://www.ncbi.nlm.nih.gov/pubmed/14533025
Embry, R., & Lyons Jr, P. M. (2012). Sex-based sentencing: Sentencing discrepancies between male and female sex offenders. Feminist Criminology, 7(2), 146-162.  Available from: http://www.ncdsv.org/images/fc_sex-basedsentencingdiscrepanciesbetweenmaleandfemalesexoffenders_2012.pdf
Women receive a broad pass when it comes to domestic violence, which distorts federal reporting and statistics on the topic
Felson, R. B., & Pare, P. (2007).  Does the criminal justice system treat domestic violence and sexual offenders leniently?  Justice Quarterly, 24, 435-459.
BJS. (1995). Bureau of Justice Statistics Fact Sheet: "Husbands convicted more often than wives for spouse murde". https://www.bjs.gov/content/pub/pdf/SPOUSFAC.PDF
Gender sentencing disparity
Doerner, J. K., & Demuth, S. (2014). Gender and sentencing in the federal courts: Are women treated more leniently?. Criminal Justice Policy Review, 25(2), 242-269. Abstract: http://journals.sagepub.com/doi/abs/10.1177/0887403412466877
Goulette, N., Wooldredge, J., Frank, J., & Travis III, L. (2015). From initial appearance to sentencing: Do female defendants experience disparate treatment?. Journal of Criminal Justice, 43(5), 406-417. Abstract: http://www.sciencedirect.com/science/article/pii/S0047235215000665
Mustard, D. B. (2001). Racial, ethnic, and gender disparities in sentencing: Evidence from the U.S. federal courts. Journal of Law and Economics, 44, 285-314 DOI: 10.1086/320276. Abstract: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=259138
As a form of institutionalized slavery and discrimination against men (and especially minority men)
BeacuseIts2015. (2017). Justice System Discrimination and the Myth That Sexism Against Men Isn’t “Institutional”. Because It's 2015. Available from: https://becauseits2015.wordpress.com/2017/01/29/justice-system-discrimination-and-the-myth-that-sexism-against-men-isnt-institutional/
Bolak, Fawn. (2017). U.S. Prison Labor and the Legacy of American Slavery. Center On Human Rights Education. Available from: https://www.centeronhumanrightseducation.org/u-s-prison-labor-legacy-american-slavery/
Discrimination against men is 6 times higher than discrimination against minorities

Summary: Same research team, same methodology, with race switched out for gender

University of Michigan: Michigan Law (2012, November 16). PROF. STARR'S RESEARCH SHOWS LARGE UNEXPLAINED GENDER DISPARITIES IN FEDERAL CRIMINAL CASES. https://www.law.umich.edu/newsandinfo/features/Pages/starr_gender_disparities.aspx

Race

Rehavi, M. M., & Starr, S. B. (2012). Racial disparity in federal criminal charging and its sentencing consequences (Working Paper No. 12-002). Ann Arbor: University of Michigan Law and Economics, Empirical Legal Studies Center. Available at SSRN: https://ssrn.com/abstract=1985377 or http://dx.doi.org/10.2139/ssrn

Gender

Starr, S. B. (2014). Estimating gender disparities in federal criminal cases. American Law and Economics Review, 17(1), 127-159.  Available at SSRN: https://ssrn.com/abstract=2144002 or http://dx.doi.org/10.2139/ssrn
Incarceration rates
INSIDE MAN. (2014). Is sexism to blame for the number of men in prison?. insideMan. http://www.inside-man.co.uk/2014/07/07/is-sexism-to-blame-for-the-number-of-men-in-prison/
Allen, R., Ashworth, A., Cotterrell, R., Coyle, A., Duff, A., Lacey, N., ... & Morgan, R. (2014). A presumption against imprisonment: social order and social values. In The British Academy. [PDF] Available from: https://www.thebritishacademy.ac.uk/sites/default/files/A%20Presumption%20Against%20Imprisonment%20updated%202016.pdf
Historical incarceration rates (from 3:1 to 20:1, indicating changes in society that disadvantage men)
The Illustrated Empathy Gap: UK Prisoners – The Genders Compared. http://empathygap.uk/?p=215
Men are more likely to receive the death penalty for the same crime and the same mitigating factors
Rapaport, E. (1991). The Death Penalty and Gender Discrimination. Law & Society Review, 25(2), 367-383. doi:10.2307/3053803
Oliver, A. (2015). The Death Penalty Has a Gender Bias. The Huffington Post. https://www.huffpost.com/entry/are-women-getting-away-wi_b_8227690
Despite these problems affecting men more than women, there are active efforts to increase these disparities in favor of women, instead of helping men
"Opinion: 8% of prisoners are women. That’s about 8% too many" (the author even seems aware that this is sexist, and tries to defend it).  The Feed. Available at: https://www.sbs.com.au/news/the-feed/opinion-8-of-prisoners-are-women-that-s-about-8-too-many
McCann, K. (2018). Justice secretary: 'Don't send women to prison unless they commit a violent crime'. The Telegraph. Available at: https://www.telegraph.co.uk/politics/2018/06/26/justice-secretary-dont-send-women-prison-unless-commit-violent/
Female offenders are treated better than male offenders, especially in prison
Stone, J. (2015). It's not fair on men that women prisoners don't have to wear uniforms, Tory MP complains.  The Independent. Available at: http://www.independent.co.uk/news/uk/politics/it-s-not-fair-on-men-that-women-prisoners-don-t-have-to-wear-uniforms-tory-mp-complains-10360347.html
DEMUTH, S., & STEFFENSMEIER, D. (2004). The Impact of Gender and Race-Ethnicity in the Pretrial Release Process. Social Problems, 51(2), 222-242. doi:10.1525/sp.2004.51.2.222
Police violence against men 
INSIDE MAN. (2015). Nine out of ten victims of police-related deaths are male. Who cares?. insideMAN. http://www.inside-man.co.uk/2015/07/24/nine-out-of-ten-victims-of-police-related-deaths-are-male-who-cares/

Police violence against men is higher than it is against minorities

Riggio, O. (2019). Police Brutality a Leading Cause of Death Among Young Men. DiversityInc. Available from: https://www.diversityinc.com/police-brutality-a-leading-cause-of-death-among-young-men/
Edwards, F., Esposito, M. H., & Lee, H. (2018). Risk of police-involved death by race/ethnicity and place, United States, 2012–2018. American journal of public health, 108(9), 1241-1248.
Number of people at risk of being killed in their lifetime by the police (per 100,000 population). Chart: African American Females and White Males circled for emphasis: https://imgur.com/a/BdBgKSU

Related issues

Sexual assault and domestic violence

Roughly 52% - 58% of rapists are estimated to be men, and around 50% of all domestic violence is committed by men. Which means there is very clear gender parity for some of these crimes. When it comes to criminality, and especially violent crime, women are more likely to target people close to them as opposed to strangers. Due to the gendered nature of these crimes, however, many people focus on male perpetration and female victimization. Which stigmatizes men as violent "abusers" while ignoring the fact that it goes both ways.

It's not just an issue of people's perceptions being biased though. There are active statutory issues codified into law as well. In many places, federally funded domestic violence programs exclude men. And sexual assault laws are often explicitly gendered.

"Gender parity for sexual assault (academic studies)". https://www.reddit.com/r/LeftWingMaleAdvocates/comments/f4v64l/gender_parity_for_sexual_assault_academic_studies/

"Some sources on the severity of domestic violence against men". https://www.reddit.com/r/LeftWingMaleAdvocates/comments/f604hw/some_sources_on_the_severity_of_domestic_violence/

False allegations and family court bias as a form of legal discrimination

False allegations, child custody discrimination, and family court discrimination are also related to the topic of legal discrimination. This represents both a gender bias in court as well as a statutory issue that needs to be addressed with legislative code changes. Some progress has been made on some of these issues, but we still have a long way to go.

"I call Bullshit on the False rape accusation sticky from Mens Lib sub. Actual lies are being told". u/Egalitarianwhistle. https://www.reddit.com/r/MensRights/comments/e6w4yc/i_call_bullshit_on_the_false_rape_accusation/

"Studies proudly posted by feminists show that men are discriminated against in family court". https://www.reddit.com/r/MensRights/comments/ecunsg/studies_proudly_posted_by_feminists_show_that_men/

2019 NPO Shared Parenting Report Card Highlights Some Progress and Great Disparity in State Custody Statutes. https://nationalparentsorganization.org/information-resources/2019-shared-parenting-report-card