At present, there are problems in teaching and teachers in colleges and universities, and college physical education and health care students do not get effective exercise, and their physical fitness indexes have decreased and mental health problems have appeared. In this paper, the effect of fitness exercise prescription on the mental health of college physical education students is the research goal, and the purpose and requirements of exercise for the students are analyzed by using questionnaires and experimental research. The effect of different exercise prescriptions on the mental health of physical education and health care students was studied. The results showed that fitness exercise prescriptions had positive effects on the mental health, physical health and hobbies of college physical education and health care students. This study provides theoretical data to support the influence of fitness exercise prescription on the mental health of college physical education and health care students.