This study aims to investigate the possible mediating and moderating factors in the relationship between peer relationships and science literacy in ethnic Zhuang adolescents, the largest ethnic minority group in China. Altogether 596 Grade 9 Zhuang students (N-female = 293, M-age = 14.74, SD = 1.38) were surveyed and tested with PISA Science (2008). The descriptive and PROCESS analyses have confirmed that motivation acted as a mediator between peer relationships and science literacy, and self-efficacy acted as a moderator. This model indicated that positive peer relationships would cause higher motivation associated with higher science literacy. Besides, self-efficacy could significantly moderate the mediation effect of motivation in females, indicating that more attention should be paid to female Zhuang students to enhance their self-efficacy and, accordingly, science literacy.