School socioeconomic status (SES) is studied primarily as a variable to explain academic achievement; however, few previous studies have investigated how SES can influence individual student's academic achievement. The present study used a national representative sample of 10,784 grade 7 to 9 students (53.2% boys and 46.8% girls) in mainland China to examine the links between school SES and students' math and Chinese achievements, including the math and Chinese teacher-student relationships as mediating factors. The parents provided family socioeconomic information and the students reported on their teacher-student relationships. Achievements in math and Chinese were assessed using standardized tests. Multilevel mediation analyses revealed that school SES was positively related to students' math and Chinese achievements. Moreover, the link between school SES and students' math achievement was partially mediated by students' perception of the math teacher-student relationship. The Chinese teacher-student relationship had no mediating effect. This study indicated that school SES can influence individual student's academic achievement via their perception of teacher-student relationship. The poverty and lack of resources is obvious, yet low SES schools could make efforts in improving teacher-student relationship's quality to promote students' academic performance. Meanwhile, low SES schools should receive more attention from policymakers to improve teaching quality and school climate. Furthermore, the study findings could be used for future research on the gap between low and high SES schools.