Objective: To investigate the association of moderate to vigorous intensity physical activity (MVPA) and screen time (ST) with emotional and behavioral problems in middle school students, so as to provide a basis for improving the mental health level of adolescents. Methods: Four public junior high schools in Jinshan District, Shanghai were selected by random cluster method from September 19 to October 18, 2023, with 779 first grade students included. Strengths and Difficulties Questionnaire (SDQ), as well as physical activity and screen time were collected. Binary Logistic regression analysis was used to investigate the association between MVPA, ST and different dimensions of emotional and behavioral problems. Results: Students with MVPA<60 min/d accounted for 82.4%, and with ST>2 h/d accounted for 29.5%. The abnormal rate of SDQ dimensions among students ranged from 6.8 % to 19.3%, with the highest abnormal rate observed in behavioral problems. The results of binary Logistic regression analysis showed that, compared with high level of MVPA, students with low level of MVPA had a significantly increased risk of developing problems in prosocial behavior [ OR (95% CI )=2.16(1.37-3.41), P <0.05]. Compared with low level ST, students with high level had an increased risk of experiencing emotional symptoms, behavioral problems and peer interaction problems [ OR (95% CI )=2.00(1.25-3.22), 2.00(1.41-2.84), and 1.69(1.22-2.33), P <0.05]. Compared with high MVPA and low ST, students with low MVPA and high ST had an increased risk of developing problems in the dimensions of conduct problems, prosocial behavior, and overall difficulty score [ OR (95% CI )=1.92(1.13-3.23), 2.73(1.56-4.77), and 2.07(1.19-3.60), P <0.05]. Conclusions Physical activity and screen time are related to emotional and behavioral problems in middle school students. Insufficient physical activity time and excessive screen time might increase the risk of emotional and behavioral problems. Interventions can be administered on physical activity and screen time among adolescents to promote their mental health.