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Objective. To classify the infection risk of human papillomavirus (HPV) among human immunodeficiency virus- (HIV-) negative men who have sex with men (MSM) using group-based trajectory modeling (GBTM). Methods. This study collected data on demographic and sexual behavior characteristics by questionnaires at semiannual visits from March 1st, 2016 to December 31th, 2017. Researchers collected anal exfoliated cells to finish HPV testing and blood samples to finish HIV testing at baseline and follow-up visits. Accumulative infection numbers of different types of HPV as the primary outcome and the follow-up visits as the independent predicator to build a GBTM model. Results. There were 500 potentially eligible HIV-negative participants at baseline, 361 (72.2%) of whom were included in this study after screening. Three trajectory groups were identified as the best-fitted GBTM model. Trajectory 1, defined as decreased group (DG) accounted for 44.6% (161/361) of the sample, showed a declining pattern with visits. Trajectory 2, defined as flat group (FG) accounted for 49.6% (179/361) of the sample, showed a flat pattern with visits. Trajectory 3, regarded as the increased group (IG) accounted for 5.8% (21/361) of the sample, showed an uptrend. Compared to the DG, risk factors for the FG included receptive anal intercourse (AOR, 2.24; 95% CI, 1.36-3.71), occasional condom use in anal sex during the past six months (AOR, 1.90; 95% CI, 1.16-3.14), experience of transactional sex with males in the past year (AOR, 3.60; 95% CI, 1.12-11.54), and substance use (AOR, 1.81; 95% CI, 1.08-3.04). Risk factors for the IG included receptive anal intercourse (AOR, 2.81; 95% CI, 1.04-7.70), occasional condom use in anal sex during the past six months (AOR, 3.93; 95% CI, 1.40-11.01), and history of other STIs (AOR, 5.72; 95% CI, 1.40-23.46). Conclusion. The MSM data in this study showed three distinct developmental trajectories (DG, FG, and IG) of HPV infection among HIV-negative MSM, with receptive anal intercourse and occasional condom use in anal sex during the past six months being the risk factors associated with FG and IG.