This study actively explores the importance of the joint construction of physical education and health courses in colleges and universities. It emphasizes its positive impact on students’ physical and mental health, talent cultivation and social development. Based on the PDCA model, the article establishes a comprehensive evaluation system, determines the weights of the indicators through the coefficient of variation method, and analyzes the cultivation of core literacy and the influencing factors using fuzzy comprehensive evaluation and structural equation modeling. The validity of the evaluation system is examined and verified with ten colleges and universities in Province L as an example, showing that the comprehensive evaluation score is as high as 95.16 points. This complete evaluation system not only helps colleges and universities to improve the quality of education, but also points out the direction for improving students’ core literacy in physical education and health.