Abstract: Objective To investigate the anal human papillomavirus (HPV) infection rate and associated factors among men who had sex with men (MSM) at the voluntary HIV counseling and testing (VCT) clinics in Shanghai, and to provide a data foundation for HPV prevention and control among this population. 【Methods】 Using convenience sampling, a questionnaire survey was conducted among MSM recruited at the VCT clinic of the Shanghai Center for Disease Control and Prevention from October 2023 to June 2024. Human immunodeficiency virus (HIV) infection was detected using the colloidal selenium method, and anal HPV infection was detected using the reverse dot-blot hybridization method. Univariate and multivariate logistic regression models were used to analyze the factors associated with anal HPV infection among MSM. 【Results】 A total of 277 participants were enrolled during the study period. After excluding 39 participants for whom typing failed due to insufficient sample cells, 238 MSM were ultimately included in the analysis. The average age ±standard deviation of the study participants was (32.9 ±9.0) years old. The proportions of participants who were unmarried (84.46%), Shanghai residents (42.44%), those with a college degree or higher (80.68%), and those who self-identified as gays (73.95%) were relatively high. The anal HPV infection rate was 37.82% (90/238), and the rate of multiple infections was 15.55% (37/238). The HPV infection rate among HIV-positive individuals was 68.57% (24/35), while among HIV-negative individuals it was 32.51% (66/203). The HPV genotypes with the highest infection rates were HPV-6 (11.76%), HPV-39 (6.30%), and HPV-52 (5.46%). The infection rate of any genotypes covered by the 9-valent HPV vaccine (HPV types 6, 11, 16, 18, 31, 33, 45, 52, and 58) was 26.05%. Multivariate logistic regression analyses showed that HIV infection (aOR = 4.07, 95% CI: 1.78–9.78), being the receptive partner in anal sex (aOR = 2.60, 95% CI: 1.19-5.82), and a history of unprotected anal sex (aOR = 2.15, 95% CI: 1.16–4.03) were positively associated with anal HPV infection, while a monthly income >10000 yuan (aOR = 0.45, 95% CI: 0.21–0.97) and awareness of HPV (aOR = 0.39, 95% CI: 0.20–0.75) were negatively associated with anal HPV infection. 84.45% (191/238) of the study participants expressed a willingness to receive the HPV vaccine; 2.10% (5/238) had already received the HPV vaccine abroad. Conclusion The anal HPV infection rate among MSM at VCT clinics in Shanghai was 37.82%, with higher infection rates observed among HIV-positive individuals, receptive anal intercourse partners, and those with a history of unprotected anal intercourse. It is recommended to strengthen HPV health education or peer education for these high-risk populations, promote the correct use of condoms and advocate for HPV vaccination, so as to thereby effectively preventing HPV transmission.