Objective: To examine the Longitudinal influence of perceived discrimination on pro social behavior of left alone junior middle school students and to explore the longitudinal mediating role of teacher-student relationship and classmate relationship, so as to provide a reference for improving pro social behavior of left behind junior middle school students. Methods: The Perceived Discrimination Questionnaire, Teacher-Student Relationship Questionnaire, Classmate Relationship Questionnaire and Prosocial Behavior Questionnaire were used to conduct two follow up surveys on 930 left behind junior middle school students in Guizhou Province at two time points, in mid November 2021(T1) and mid May 2022(T2). Deviation corrected Bootstrap method was used to examine the mediating effect of T2 teacher-student relationship and T2 classmate relationship on the impact of T1 discrimination perception on T2 pro social behavior. Results: The perceptions of discrimination, teacher-student relationship, classmate relationship, and pro social behavior scores of the left behind junior high school students were (1.98±0.94) (4.13± 0.77 ) (3.54±0.91) (3.52±0.75) for T1, and (3.98±0.83)(3.42±0.86)(3.48±0.72) for teacher-student relationship, classmate relationships and pro social behavior scrores of T2. After controlling for gender, age and self assessment of family economic status, T1 perceived discrimination negatively predicted T2 pro social behavior ( β =-0.07); and T1 perceived discrimination indirectly influenced T2 pro social behavior through T2 teacher-student relationship, and mediated effect value was -0.02(95% CI = -0.02 to -0.01); and T1 perceived discrimination indirectly influenced T2 pro social behavior through T2 classmate relationship, mediated effect was -0.03(95% CI =-0.05 to -0.02)( P <0.05). Conclusions Perceived discrimination not only directly reduces pro social behavior of left behind junior middle school students, but also indirectly and negatively affects pro social behavior of left alone junior middle school students by reducing teacher-student relationship and classmate relationship.