This study aimed to explore the prevalence of tobacco use, alcohol consumption, illegal substance use, social victimization, and physical violence and their associations. A cross-sectional survey was conducted among 1,050 undergraduate students in Thailand who self-identified as LGBTQ. The data was collected using an online questionnaire. The prevalence of substance use among LGBTQ undergraduate students in Thailand over the past 30 days varied, with alcohol use at 58.3%, tobacco use at 19.2%, and illicit drug use at 8.0%. Additionally, 28.4% of LGBTQ undergraduate students reported experiencing social victimization, while 7.4% indicated experiencing physical violence based on gender identity. Factors such as lower GPA, social victimization, and physical violence were all associated with increased use of tobacco, illicit drugs, and alcohol among LGBTQ students, except for violent experiences, which were not significantly related to alcohol use. The use of both legal and illegal substances is a prevalent issue among LGBTQ undergraduate students in Thailand and is associated with social victimization and physical violence. Therefore, universities and public health agencies urgently need to design measures to monitor and address these issues among LGBTQ identified students to effectively break negative cycles.