Anal HPV infection is particularly prevalent among men who have sex with men (MSM). The purpose of this study was to understand the status and influencing factors of HPV infection in MSM in Urumqi, Xinjiang, in order to provide suggestions for policy formulation. A prospective cohort study was conducted among HIV-negative MSM in Urumqi Xinjiang between April 2016 and June 2023. 824 MSM were recruited. Data were collected anal swab results from self-administered questionnaires and laboratory tests. A Cox regression model was employed to analyze factors associated with HPV infection. The prevalence rates of high-risk HPV and low-risk HPV were 37.99% and 25.97%. Receptive anal intercourse is a well-established risk factor for both incident and persistent HPV infections among MSM. For new high-risk HPV infections, the adjusted hazard ratio is 1.55 (95% CI: 1.28-1.89), and for persistent high-risk HPV infections, the aHR is 1.95 (95% CI: 1.48-2.57). Similarly, for low-risk HPV, receptive anal intercourse increases the risk of incidence (aHR = 1.34, 95% CI: 1.07-1.67) and persistent infection (aHR = 1.64, 95% CI: 1.18-2.29). Seeking sexual partners in bathhouses raised the risk of low-risk HPV infections (aHR = 1.36, 95% CI: 1.05-1.76). Young MSM may face a higher risk of HPV infection. Implementing targeted HPV vaccination catch-up programs for the MSM population in Urumqi could offer significant societal benefits.