Background Young Black and Latinx sexual minority men (SMM) and transgender women (TW) continue to suffer some of the highest burdens of HIV in the United States. Disparities are partly attributed to suboptimal uptake of HIV prevention and treatment services negatively impacted by substance use. Adult studies have demonstrated that polysubstance use increases HIV acquisition risk through increased sexual behaviors, however there are few studies that have examined polysubstance in this population and how polysubstance use might increase risk for HIV among young SMM and TW. Methods Cross-sectional data from 466 young Black and Latinx SMM and TW living in four US high HIV-burden cities enrolled in the PUSH Study, a status neutral randomized control trial to increase uptake of pre-exposure prophylaxis and treatment adherence. Examined data for patterns of polysubstance use comparing age differences of use; and exploring associations between substance use and HIV risk behaviors focusing on three core partnership factors - inconsistent condom use, pressure to have anal sex without a condom, and older partner. Results Most participants described prior substance use with alcohol and cannabis being most common (76%, respectively) and 23% describing other describing prior alcohol use, 76% (n=353) described cannabis use, and 23% described other illicit drug use (including stimulants, cocaine, hallucinogens, sedatives, opioids, and inhalants). Polysubstance use was common with nearly half (47%) of participants reported alcohol and cannabis use, 20% reporting alcohol, cannabis, and one other illicit drug use, and 19% reporting alcohol or cannabis use plus one other illicit drug use. Polysubstance use was associated with greater adjusted odds of pressure to have anal sex without a condom, having an older partner (> 5 years older), and inconsistent condom use. Conclusions High levels of substance use, polysubstance use and strong associations with high-risk sexual practices and sexual partnerships that are known to be predictors of HIV acquisition or transmission among Black and Latinx sexual and gender minority youth, call for combination interventions that include substance use treatment alongside ARV-based prevention and treatment and partner-based interventions.