Objective: To explore mental health status of vocational college students and its association with physical exercise and exercise motivation, so as to provide data support for the promotion of physical exercise, exercise motivation theory and the protection of mental health among vocational college students. Methods: From June 2 to July 2, 2023, a convenience sampling method was used to select 1 763 college students from three vocational colleges in Sichuan, Chongqing, and Guizhou for the survey. Physical Activity Rating Scale (PARS-3), Motives for Physical Activities Measure-Revised (MPAM-R), Patient Health Questionnaire-9 (PHQ-9) and Flourishing Scale (FS) were used to assess physical exercise, exercise motivation, depressive symptoms and flourishing levels of vocational college students. Multiple linear regression analysis was conducted to examine the relationship between physical exercise, exercise motivation, depression as the negative indicator of mental health and flourishing as the positive indicator of mental health. Results: There were negative correlations between physical exercise, exercise motivation and their five factors with depression scores among vocational college students ( r=-0.162--0.133, P <0.01). Physical exercise, health motivation and pleasure motivation were positively correlated with flourishing and its eight factors among vocational college students ( r= 0.054 -0.099, P <0.05). Depression scores and flourishing scores varied significantly across students with different levels of physical exercise and exercise motivation ( F=11.18-15.69, 2.80-16.05, P <0.05). Multiple linear regression analysis indicated that physical exercise, health motivation, and total exercise motivation scores were negatively correlated with depressive symptoms ( β = -0.02 , -0.11, -0.35), and physical exercise, health motivation, pleasure motivation, and total exercise motivation scores were positively correlated with flourishing ( β =0.31, 0.32, 0.50, 0.30) ( P <0.05). Conclusions Physical exercise and exercise motivation are significantly associated with mental health of vocational college students. Enhancing physical exercise and increasing exercise motivation in aspects of health and pleasure can promote mental health of vocational college students.