Objective: To analyze the intervention effects of moderate to vigorous classroom physical exercise on psychological sub health among Uyghur junior high school students, providing reference for mental health promotion and intervention in the ethnic group. Methods: From April to July 2022, 647 eighth grade Uighur junior high school students from two middle schools in the Kashgar Prefecture, Xinjiang, were selected using a random cluster digital sampling method. They were randomly assigned to a control group ( n =326) and an intervention group ( n =321). While adhering to the regular curriculum, the intervention group additionally received 12 week, 36 session (every Monday, Wednesday, and Friday afternoon) moderate to vigorous classroom physical exercise intervention (45 minutes per session, including warm up, main exercises, and cool down activities). Self administered psychological sub health was completed through Brief Instrument on Psychological Health of Youths before and after intervention, and the data were analyzed using covariance analysis. Results: Before intervention, there were no statistically significant differences between the control and intervention groups in the total scores for psychological sub health or in the scores for the three dimensions including emotional problems, conduct problems, and social adaptation difficulties ( t =0.76, 0.40, 0.01, 0.94 , all P >0.05). After intervention, the scores of the intervention group s junior high school students on the emotional problems, conduct problems, and social adaptation difficulties dimensions decreased by 0.50, 0.28, and 0.18, respectively, compared with the control group, and all differences were statistically significant ( t =3.35, 3.36, 2.07, all P <0.05). The main effect of the psychological sub health category was statistically significant ( F =60.66, P <0.01, partial η 2=0.09). Compared with the control group, the psychological sub health scores of junior high school students in the intervention group decreased by 0.96 ( t =3.42, P < 0.05 ). Conclusion The 12 week moderate to vigorous classroom physical exercise intervention has a positive effect on the psychological sub health of Uyghur junior high school students.