The purpose of this study was to explore the influence of different exercise intervention methods and health education on students’ physical and mental health, so as to help the disadvantaged primary school students choose scientific and reasonable physical exercise methods. Research methods: A total of 80 students from the fifth grade of Xiaogan Experimental Primary School were randomly selected to participate in this study according to the physical fitness test results. The experimental group received exercise intervention and health education for one semester, while the control group did not receive any intervention. Results: After exercise intervention and health education, the body shape of obese and thin primary school students in the experimental group gradually became normal; The Angle of pelvis forward is decreasing and the scoliosis is approaching the neutral position. The heart rate of the students decreased and their vital capacity increased significantly when they were quiet. After intervention, the 50 m running time of primary school students was shortened, the number of skipping rope per minute was increased, and the mean of sitting forward bend was increased significantly, showing significant differences compared with before intervention (p<0.05). In terms of mental health, there were significant differences between the experimental group and the control group in terms of subjective experience and physical value, with statistical significance (p<0.01). Conclusion: Exercise intervention and health education can improve the physical form, physical function, physical quality and mental health of primary school students in different vulnerable groups.