Human papillomavirus (HPV) infection among men who have sex with men (MSM) in China is underreported. We performed a systematic review and meta-analysis to clarify site-specific HPV prevalence among MSM in China. We searched both English and Chinese databases for all studies published before April 1, 2020, that reported HPV prevalence among MSM in China. Random-effects meta-analysis was used to calculate summary estimates. Thirty-four articles were eligible, where 32, 5, and 2 articles reported HPV prevalence at the anus, penis, and oral cavity, respectively. The estimated prevalence of anal HPV among MSM in China was 85.1% (HIV-positive), 53.6% (HIV-negative), and 59.2% (unknown HIV status), with HPV genotypes being predominated by HPV 6, 11, 16, 18, 52, and 58. Any HPV and high-risk (HR) HPV was more common in northern China, while low-risk HPV was more common in southern China. HPV prevalence increased with age among HIV-negative MSM, from 40.5% (aged < 20 years) to 57.2% (aged ≥ 40 years). High prevalence of any HPV (HIV+: 95.1%; HIV-: 97.7%) and multiple infections (HIV+: 75.9%; HIV-: 41.7%) was found in anogenital warts among MSM. HPV is common among MSM in China. MSM living with HIV and/or anogenital warts were at disproportionate risk for HR HPV. Younger MSM were found to have a lower HPV prevalence. HPV vaccines would have prevented the majority of infections if given before sex debut. HPV at anatomical sites other than the anus, incident HPV infection, and the cost-effectiveness of HPV vaccination in this population are worth further investigation.