Objective: To understand the infection status and elimination of anal human papillomavirus (HPV) among men who have sex with men (MSM) in Urumqi, Xinjiang. Methods: The sample size formula in cohort study, a dynamic cohort study method, was used, with the sample size estimated to be 712 according to the new infection rate of HPV16. With the help from non-government organzitions in Urumqi, we recruited 810 MSMs by the snowballing method, and a follow-up program was carried every six months. Anal exfoliated cells were collected to analyze HPV type 16 and 18 infection rates. For statistical analyses, Poisson regression was used to estimate the density of new infections and persistent infections. Cox proportional hazard model was used to explore the influencing factors on both new and persistent infections and the diseases' natural clearing. Results: A total of 810 MSM were recruited, and 482 MSMs with the number of follow-ups more than 2 times were included in the analysis, with the total follow-up numbers as 994.7 person-years. The median number of follow-up and follow-up times was 4 (P25,P75:3,5) times , and 2.2 (P25,P75:1.8, 2.6) years. The baseline infection rates of HPV16 and HPV18 were 8.5% (41/482) and 3.3% (16/482), respectively. And the baseline mixed infection rate of the two types was 0.6% (3/482). The first new infection densities of HPV16 and HPV18 were 10.06 (95%CI:8.12-12.45)/100 person-years and 5.24 (95%CI:3.95-6.96)/100 person-years. The rate of natural infection clearance of HPV16 and HPV18 were 71.2% (89/125) and 71.8% (46/64), respectively. The natural clearance rate of HPV18 after 1.5 years follow-up was higher than HPV16 (97.7% vs. 94.1%). The persistent infection rate of HPV16 and HPV18 were 4.5% (20/441) and 1.7% (8/466), respectively. The risk of persistent HPV16 infection among unmarried subjects was lower than that of married subjects (aHR=0.29,95%CI:0.12-0.71). The natural clearance rate of HPV18 without condom use in anal intercourse in the last six months was 2.63 times higher than that of condom use (95%CI:1.08-6.42). Conclusions: HPV16 and 18 new infections are more common among MSM in Urumqi, and the natural clearance rate is higher. Compared with HPV18, HPV16 has a higher density of new and persistent infections, a low natural clearance rate, and a greater risk of the diseases.