Objective To systematically review the intervention effect of physical exercise on mental health problems of left-behind children in rural areas, and provide suggestions for the mental health prevention and treatment of left-behind children. Methods We searched literature till June 2022 of physical exercise intervention on mental health problems of rural left-behind children published in Chinese and English in databases, such as CNKI, Vip, and Web of Science. Three-level meta-analysis was conducted by using the R package metafor. Results A total of 8 articles were included and analyzed, with a total sample size of 579 people, 288 in the experimental group and 291 in the control group. The metaanalysis results indicated that after physical exercise, the mental health of left-behind children significantly improved（g=-0.648 7, 95%CI -0.924 5 --0.372 9, P<0.001）. Meta-regression results showed that there were significant moderating effects of the participants’age（Q=4.052, P<0.05）, frequency of exercise（Q=4.608, P<0.05）, and number of exercise types（Q=6.667, P<0.01）. Conclusion The mental health of rural left-behind children can be effectively improved through physical exercise.