Given the significant increase in discrimination against Chinese Americans since the outbreak of the COVID-19 pandemic, this study examined the changes in profiles of mental health problems and school engagement among Chinese American adolescents (N = 206, MAge = 14.42) during the pandemic. Two waves of online surveys including questions about mental health problems, school engagement, COVID-19-related peer discrimination, and social-emotional competencies (SECs) were conducted in May and October 2020. A latent transition analysis of Chinese American youths’ mental health problems and school engagement suggested that participants could be classified into two profiles: troubled (higher mental health problems, lower school engagement) and complete well-being profiles (lower mental health problems, higher school engagement). Students’ transition from troubled to complete well-being profiles was associated with lower levels of COVID-19-related peer discrimination. However, students’ SECs did not predict the profile transitions. It highlights the urgent need for interventions to address and mitigate discrimination experiences within the Chinese American adolescent population.