Objective To explore the pre-exposure prophylaxis (PrEP) risk compensation of men who have sex with men (MSM) and the intervention of human immunodeficiency virus (HIV) self-testing on relevant risk behaviors in Chongqing. Methods Eligible MSM were recruited in Chongqing from Jun. 2018 to Jun. 2019. Truvada (Emtricitabine and Tenofovir Disoproxil Fumarate tablets) was prescribed as the PrEP drug of choice, and the subjects were randomly assigned at a ratio of 1:1 (by drawing lots) into HIV self-testing intervention group and control group. After 6 months of follow-up, the effect of HIV self-testing on PrEP risk compensation was investigated. Results A total of 126 subjects were included, and 93 eventually completed the study, including 43 in the HIV self-testing group and 50 in the control group. There was no significant increase in PrEP related risk behaviors during the follow-up period, but the number of participants who were engaged in receptive penetrative sex, the number of participants who had unprotected anal sex with partners having unknown HIV status, and the incident rate of new sexually transmitted diseases all showed an increasing trend. In addition, the proportions of subjects with condom use rate<50% in the HIV self-testing group were significantly higher than those in the control group (P=0.035, P=0.043) at the 3^rd and 6^th months of follow-up. Conclusion PrEP-related risk behaviors of MSM in Chongqing do not show a significant increase at 6 months of follow-up. However, some risk behaviors show an upward trend. MSM who use HIV self-testing may have risk compensation behaviors, which should be alerted and education should be strengthened.