To analyze the incidence of HIV infection and identify associated risk factors in drug abusers among men who have sex with men (MSM) in Tianjin and Shanghai through a cohort study and provide a basis for HIV prevention in this population. A prospective cohort study was conducted among MSM who had a history of drug abuse in the past six months from June 2016 to June 2018 in the two cities. MSM were investigated to obtain information on sociodemographic characteristics, HIV-related sexual behaviors, and drug abuse. Follow-up investigation and HIV testing were carried out based on the baseline survey and testing. Cox regression analysis was conducted to identify the risk factors for HIV infection. There were 455 eligible subjects, and 16 new HIV infection cases were identified in the 2-year follow-up survey. The cumulative follow-up time was 586.08 person-years, and the incidence of HIV infection was 2.73/100 person-years. The multivariate Cox regression analysis results showed that compared with those aged ≥25 years, consistent condom use during anal sex with men in the past six months, without mixed-use of drugs, these aged <25 years (=5.01, 95%: 1.09-23.11), inconsistent condom use during anal sex with men in the past six months (=1.58, 95%: 1.04-2.41) and mixed-use of drugs (=1.92, 95%: 1.08-3.40) were significantly associated with HIV infection in this cohort. The younger age, inconsistent condom use during anal sex with men, and mixed drug use appeared as risk factors of new HIV infection in drug abusers among MSM. HIV prevention and intervention in this population should be further strengthened.