Several studies have shown that individual-level collectivism among ethnic minority migrant students hinders their adaptation to Western societies, whereas individualism facilitates adaptation. However, it is uncertain whether these effects apply to Chinese ethnic minority students’ adaptation to nation-dominated regions in China. Additionally, most studies examining the influence of cultural values on the adaptation of minority students have generally employed cross-sectional designs, and there has been a lack of investigation into the mediating mechanisms of this influence. Therefore, this study aims to investigate the longitudinal impact of individual-level collectivism and individualism on Chinese ethnic minority students’ adaptation and the mediating role of emotion regulation. Data on individualism, collectivism, school adaptation, depression, and anxiety were collected from 447 first-year high school minority students who migrated from Xinjiang to Hangzhou at two time points (T1: September 2022; T2: March 2023). The results revealed that individual-level collectivism positively predicted school adaptation and negatively predicted depressive symptoms six months later. In contrast, individualism negatively predicted school adaptation and positively predicted anxiety symptoms after six months. Furthermore, cognitive reappraisal mediated the impact of collectivism on adaptation, whereas expressive suppression mediated the impact of individualism on adaptation. The results demonstrated that collectivism encourages Chinese ethnic minority students to employ cognitive reappraisal, thereby facilitating adaptation, whereas individualism encourages them to employ expressive suppression, hindering adaptation.