Objective: To investigate the relationship between after-school schedule and bone mineral density in middle-school students in Shanghai, to provide a reference for taking targeted measures. Methods: From November 2017 to April 2018，eighteen classes of six middle schools in Shanghai (from urban districts, urban-suburb combined districts and suburban districts, respectively) were selected based on cluster random sampling. In each school, 2-4 classes were further randomly chosen in the 6th grade. Questionnaires were completed by 518 students and their parents, as well as physical examination and bone mineral density assessment. Results: The average time spent on after-school academic learning during weekends was 4.0 (IQR: 2.0, 6.0) h. The Z-score of bone density was 0.3 (IQR: -0.7, 1.0). The smooth curve fit model showed a non-linear relationship between after-school academic learning time during weekends and the Z-scores of bone mineral densities. A two-stage multiple linear regression analysis was further applied according to the fit results, and the results showed that when total afterschool academic learning time <4.5 hours during weekends, the learning time was inversely correlated with the bone density Z-scores (β=-0.11,P=0.01), and when the learning time ≥4.5 hours, there was no significant correlation between the learning time and bone density Z-scores (β=0.02, P=0.65). Parent and student questionnaires showed that there was a non-linear relationship between students’ daily time spent on outdoor sports-related activities and bone density Z-scores. When time spent on the outdoor activities ≥45 minutes per day, outdoor activities were positively correlated with bone density Z-scores (P<0.05). However, when the time spent on outdoor activities <45 minutes per day, there was no significant relationship between outdoor activities and bone density Z-scores (P>0.05). Conclusion Too much time on after-school academic learning during weekends or limited time on outdoor activities are both related to impaired bone mineral densities. Therefore, a reasonable after-school schedule for middle-school students is important for physical development, especially during weekends.