Internalized sexual stigma (ISS) is one of the major issues that can compromise the health of sexual minority populations. This quantitative study aimed to examine: (1) the relationships of individual factors (gender, age, education level, sexual orientation, and age of identification of sexual orientation) and perceived family support with ISS; and (2) the associations of ISS with mood problems and the moderating effects of gender on the associations among Taiwanese young adult lesbian, gay, and bisexual (LGB) individuals. In total, 500 male and 500 female young adult LGB individuals aged between 20 and 30 years participated in this study. The experience of ISS, individual (e.g., gender, age, education level, sexual orientation, and age of identification of sexual orientation) and environmental factors (perceived family), mood problems (e.g., anxiety and depression) were collected. The individual and environmental factors related to ISS and the associations of ISS with mood problems were examined using multivariate linear regression analysis. The results indicated that gender, sexual orientation, age of identification of sexual orientation, and perceived family support were significantly associated with all or some dimensions of ISS in LGB individuals. Various dimensions of ISS had different relationships with anxiety and depression. Gender had moderating effects on the association between the identity dimension of ISS and sexual orientation as well as between the social discomfort dimension of ISS and anxiety. Various dimensions of ISS among LGB individuals should be routinely assessed by mental health service units. Intervention programs should be provided for LGB individuals, especially those with factors related to ISS.