HIV prevalence is higher among Men who have Sex with Men (MSM), owing to their unsafe sexual behavior. Further, MSM indulge in behaviors such as consumption of alcohol/oral drugs and/or injecting during/before sex that poses the risk of unsafe behaviors, thereby increasing their vulnerability to HIV. The study aims to analyze the factors associated with HIV infection among the multi-risk MSM using any substances with those MSM who do not use substances.Community-based cross-sectional survey design using probability-based sampling between October 2014 and November 2015.For the nation-wide Integrated Biological and Behavioral Surveillance (IBBS), 23,081 MSM were recruited from 4067 hotspots in 108 districts across India. Information on demographics, sexual behaviors, substance use, sexual partners, and awareness on HIV and its management was collected from the consented respondents using computer-assisted personal interview (CAPI) by trained personnel. Blood samples were tested for HIV. Statistical analyses were done, to study the associations between substance use and its influence on high-risk sexual behaviors and HIV infection.One in 3 MSM (33.88%) in India were substance users, thus exhibiting "multi-risk" (MR) behaviors. Significantly higher HIV prevalence (3.8%, P < .05) was reported among MR-MSM, despite 97.2% of them being aware of HIV. Higher HIV prevalence among MSM exhibiting homosexual behavior for ≤1 year is of specific concern, as this accounts to recent infections and indicates the increased vulnerability of the infection among the new entrants.Substance-use resulting in high-risk sexual behavior was significantly associated with higher HIV prevalence among MR-MSM. Integrated targeted interventions focusing on safe sex and safe-IDU practices among MR-MSM are required to end the disease transmission.