School is the primary setting for social activities among adolescents, and the quality of school adjustment has a significant impact on their physical and mental well-being. Research has shown that perceived social support, school belongingness, and physical activity can influence adolescents' school adjustment, but the underlying mechanisms remain unclear. From March to December 2023, 1167 adolescent students (595 males and 572 females) with an average age of 13.68 ± 0.88 years old in Shandong Province of China were surveyed with a psychological questionnaire by cluster stratified sampling method and through the construction of PLS-SEM to explore the relationship between perceived social support, school belongingness, and physical activity on school adjustment. The results indicated that perceived social support directly predicts middle school students' school adjustment and indirectly predicts it through the mediating variable of school belongingness. Additionally, it was found that individual levels of physical activity moderate the first half of the mediating path from school belongingness to school adjustment. This finding emphasizes the important roles of perceived social support, school belongingness, and physical activity in facilitating successful school adjustment among adolescent students. Based on this finding, it provides new suggestions for policy-makers in the face of adolescents who can not adjust to school life and have the tendency to drop out.