Background: Although the general role of the school social environment in academic motivation has been demonstrated by many researchers, less attention has been paid to the effects of peer relationships, especially opposite-gender peers, on academic motivation, and the mechanisms of interaction between the two are unclear. Method: The present study explored the longitudinal relationship between adolescents’ opposite-gender peer relationships and students’ motivation through a four-wave longitudinal study of 2,380 students (52% female) using the random intercept cross-lagged panel modeling (RI-CLPM) method. Results: The results of the study revealed gender differences: for boys, opposite-gender peer relationships were positively associated with academic motivation, whereas this effect was not significant among girls, and there was no cross-lagged effect. Conclusion: The study aims to enlighten educators to pay attention to gender differences among adolescents by exploring the interactions between peer relationships and academic motivation, to enhance researchers’ understanding and practice of the link between students’ peer relationships and motivation, and to cultivate optimal social environments for students’ learning.