Affiliating with an aggressive peer group has various negative implications for individual development and adjustment, and adolescents are particularly vulnerable to negative peer influence. It is crucial to identify factors that serve to protect adolescents who are members of aggressive peer groups. Autonomy is an important individual characteristic worth exploration because it captures adolescents’ differences in navigating their group experiences and it is closely related to their developmental tasks during this period. Moreover, autonomy has become increasingly important in Chinese society in recent years during the rapid social change. The purpose of the present study was to examine the relations between group-level aggression and social, behavioral, school, and psychological adjustment, as well as the moderating role of individual autonomy in shaping these associations in a sample of Chinese adolescents. Participants included 1742 students (821 boys) in Grade 7 (mean age = 13.40 years, SD = .58) and Grade 10 (mean age = 16.32 years, SD = .54) from six regular public schools in China. Data were collected from multiple sources. The participants completed a measure of peer group networks and self-report measures of autonomy, depression, loneliness, and problem behaviors. In addition, peer nominations and teacher rating were used to assess adolescents’ social competence, learning problems, aggression, and externalizing problems. Information on academic achievement was obtained from school records. The results showed that group-level aggression was positively related to maladjustment in social, behavioral, and academic domains and that the positive relation of group-level aggression and deviancy and the negative relation of group-level aggression and academic functioning were moderated by individual autonomy. Group-level aggression was associated with deviancy and academic functioning to a lesser extent among adolescents who were higher on autonomy. These results have implications for parents, educators, and professionals who aim to help adolescents affiliated with aggressive peer groups.