Background <p>China has reported a high rate of HIV transmission through male-to-male sexual contact. This study aims to update the trend in HIV incidence density and identify associated risk factors among men who have sex with men (MSM) in Chongqing, China.</p> Methods <p>Data on HIV incidence and sexual behaviors were obtained from the Chongqing CDC for MSM from 2013 to 2022. HIV incidence density was calculated biennially, along with the overall incidence rate. Cox proportional hazards regression was used to identify risk factors associated with HIV infection.</p> Results <p>A total of 2,134 HIV-negative MSM were included in the cohort. The overall HIV incidence density was 4.9 (95% CI: 4.3–5.6)/100 person-years (PYs) from 2013 to 2022. The HIV incidence density among MSM showed a declining trend. Multivariable analysis showed that MSM with a high school education or below (HR 1.57, 95% CI: 1.21–2.03), an anal sex role of versatile (HR 1.38, 95% CI: 1.03–1.85), seeking male sexual partners through offline methods (HR 1.73, 95% CI: 1.34–2.23), engaging in unprotected anal intercourse (HR 1.53, 95% CI: 1.19–1.97), and using rush poppers in the past six months (HR 1.60, 95% CI: 1.09–2.33) were identified as significant risk factors associated with HIV infection.</p> Conclusion <p>The decline in HIV incidence density among MSM from 2013 to 2022 appeared to reflect the impact of comprehensive HIV prevention strategies implemented in Chongqing. Continued efforts to raise awareness of HIV infection, promote condom use, and reduce high-risk sexual behaviors among MSM remain essential public health priorities.</p> Clinical trial <p>Not applicable.</p>