Objective: To investigate the causal relationship between junior high school students aggressive behavior, physical exercise and academic performance, so as to provide a reference basis for the development of scientific exercise programs. Methods: A longitudinal followup study was conducted on 502 junior high school students over a 12month period from June 2021 to June 2022 using the Buss-Perry Aggressive Questionnaire (BPAQ), Physical Activity Questionnaire for Adolescents (PAQ-A), and test scores as the measurement tools (T1:June 2021, T2:December 2021, T3:June 2022), and a crosslagged model was constructed to measure the relationship between aggression, physical activity and academic performance. Results: At T1, physical exercise had a positive effect on academic performance at T2 (β=0.22) and a negative effect on aggressive behavior at T2 (β=-0.13), aggressive behavior negatively affected academic performance at T2 (β=-0.23), and academic performance had a negative effect on aggressive behavior at T2 (β=-0.09). Physical exercise at T2 had a negative effect on aggressive behavior at T3 (β=-0.05) and a positive effect on academic performance at T3 (β=0.19). Aggressive behavior at T2 negatively influenced academic performance at T3 (β=-0.08). Academic performance at T2 negatively influenced aggressive behavior at T3 (β=-0.06) (P<0.05). The results of crosslagged modeling of junior high school students aggressive behavior, physical exercise and academic performance showed that the model was well fitted (χ2/df=8.80, CFI=0.96, NFI=0.95, RFI=0.87, IFI=0.96, TLI=0.88, RMSEA=0.12). The results of multigroup structural equation modeling showed that the differences between the models and the baseline model (CFI=0.95, TLI=0.86, RMSEA=0.10, 90%CI=0.08-0.11, P<0.01) were not statistically significant in terms of gender (△CFI<0.05, P>0.05). Conclusions Physical exercise negatively predictes aggressive behavior and positively predictes academic performance, and academic performance and aggressive behavior negatively affect each other. A scientific exercise program should be developed to reduce aggression and effectively improve adolescents academic performance.