Abstract: Objective To explore the effect and associated factors of physical exercise on the physical and mental health among college students.Methods A total of 240 male and female students who were physically inactive were selected from a university in Nanjing, randomly divided into the intervention (160) and control group (80).Physical examination was carried out before and after the intervention, including height, weight, waist circumference, hip circumference, heart rate, diastolic blood pressure, systolic blood pressure and lung capacity.Body mass index (BMI), waist-to-hip ratio (WHR) and vital capacity index was calculated.The mental health condition was measured by SCL-90 scale.The students of the intervention group were matched according to clustering analysis, which was divided into the effective group and the poor effect group.Results Compared with the control group, there were statistically significant differences in BMI, heart rate, systolic blood pressure and lung capacity in the intervention group (P<0.05), and there were statistical differences in the four dimensions of coercion, interpersonal relationship, depression and hostility in the SCL-90 scale (P<0.05).Rural origin, the weekly exercise frequency was 1, frequent colds and not afraid of sports were protective factors for better intervention effects (OR> 1.0).The students who were unable to continue to adhere the sports said the main reason was the dislike of the sports type (60.71%), dislike of the feeling of failure in sports (54.72%), or no time (36.90%).Conclusion Short-term exercise intervention in college students has a positive effect on physical and mental health.Targeted exercise prescription should be done for different population characteristics.Increasing the sports fun can improve the effect of exercise intervention.