The aims of this cross-sectional survey study were to examine the association between sexual orientation microaggression and anxiety and depression among young adult lesbian, gay, and bisexual (LGB) individuals in Taiwan, as well as to examine the mediating effect of self-identity disturbance and the moderating effect of gender. In total, 1000 self-identified LGB individuals participated in the study. The experience of sexual orientation microaggression was assessed using the Sexual Orientation Microaggression Inventory, self-identity disturbance was assessed using the Self-Concept and Identity Measure, anxiety was assessed using the State subscale on the Chinese version of the State-Trait Anxiety Inventory, and depression was assessed using the Center for Epidemiological Studies-Depression Scale. Structural equation modeling (SEM) was used to examine relationships between the variables. The SEM results demonstrated that sexual orientation microaggression was directly associated with increased anxiety and depression, as well as being indirectly associated with increased anxiety and depression via the mediation of self-identity disturbance among young adult LGB individuals. Gender did not moderate the relationships between any of the variables. Both sexual orientation microaggression and self-identity disturbance warrant program interventions for enhancing mental health among LGB individuals.