Objectives: This study explored the relationship between physical activity (PA), body mass index (BMI), and physical fitness among junior high school students in Shanghai. Methods: A nationwide offline survey was conducted in Shanghai between August and December 2023, using a purposive sampling design. A total of 403 questionnaires were administered to 10 ninth-grade classes in 10 schools in Shanghai and 372 responses were included in the final analysis. Smart-PLS 4.0, structural equation modeling techniques were employed to analyze the collected data. Results: Light physical activity (LPA) had no influence on BMI, 800/1000 m (800/1000 M), sitting forward bend (FB), standing long jump (SLJ), 50 m (50 M), or vital capacity (VC). The results of part hypothesis supported the hypothetical model and explained that BMI had a negatively influence on 50 M, 800/1000 M and SLJ, BMI had a positively influence on VC. Moderate physical activity (MPA) had a negatively influence on BMI, but vigorous physical activity (VPA) had a positively influence on BMI, they both had influence on 50 M and FB, but had no influence on 800/1000 M, SLJ, and VC. Conclusions: BMI, MPA and VPA were found as pivotal factors influencing physical fitness, MPA and VPA were found to have divergent effects on BMI. This study highlighted the multifaceted nature of the relationship between PA, BMI, and physical fitness in junior high school students in Shanghai.