Anal human papillomavirus (HPV) infection, which is linked to anal warts and anal cancer, is common among men who have sex with men (MSM), especially among those HIV positives. MSM aged 18 years or older were recruited from mainland China. Blood and anal cytologic samples were collected for HIV-1 serological test and HPV genotyping. A total of 889 eligible participations were included. The genotyping results of HPV were available for 822 participants (92.46%), 65.32% of which were positive for the targeted 37 HPV types. Prevalence of infection with any type of HPV was higher among HIV-infected participants (82.69%) as compared to HIV-uninfected participants (62.81%) (p < 0.01). HPV06 (15.45%), HPV18(13.50%), HPV16 (11.44%), and HPV11 (10.71%) were the most frequent types identified in the study population. Ever had paid sex with man was found to be independent predictor for HPV positivity with an adjusted odds ratios (OR) of 2.34 (1.16-4.74). Anal HPV positivity was observed to be independently associated with HIV infection with an adjusted OR of 3.03 (1.76-5.21) in the study population. In conclusion, the prevalence of anal HPV infection was observed to be common among MSM from mainland China, and it was significantly associated with the status of HIV infection.