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Human papillomavirus (HPV) infection causes multiple cancers in both women and men. In China, both HPV vaccination and cervical cancer screening coverages are low. We aim to investigate the temporal and geographical trends of HPV DNA prevalence in heterosexual men, women, men who have sex with men (MSM) and people living with HIV (PLHIV) in China.We conducted a systematic review, collecting publications in PubMed, Web of Science, China National Knowledge Infrastructure (CNKI) and Wanfang Data from January 2000 to May 2017. A total of 247 studies were selected for this meta-analysis to estimate pooled HPV prevalence, incidence of cervical cancer and risk of infection for subgroups. Meta-regression was applied to identify contributing factors to prevalence heterogeneities.The national HPV prevalence was 15.6% (95% CI (14.4% to 16.9%)) in women with normal cervical cytology, and Central China had the highest prevalence (20.5% (15.2% to 25.8%)). HPV prevalence in heterosexual men (14.5% (11.3% to 17.7%)) was comparable with that of women (OR=1.09 (0.98 to 1.17)), but HPV prevalence in MSM (59.9% (52.2% to 67.6%)) was significantly higher than that in heterosexual men (OR=8.81 (8.01 to 9.69)). HIV-positive women (45.0% (38.4% to 51.6%)) and HIV-positive MSM (87.5% (82.3% to 90.9%)) had 4.67 (3.61 to 6.03) and 6.46 (5.20 to 8.02) times higher risk of HPV infection than their HIV negative counterparts.HPV infection is prevalent in China, particularly in Central China, in comparison with the global level and neighbouring countries. Targeted HPV vaccination for women, MSM and PLHIV and scale-up of cervical screening for women are priorities in curbing the HPV epidemic in China.