Physical education in colleges and universities is of great significance to the development of the whole education chain, to realize the goal of physical education courses in colleges and universities and to promote the physical and mental health development of students, this paper takes the physical education courses and students in Z college and university as the object of research, and proposes a correlation model of the physical education courses in colleges and universities and students’ health status by combining the fuzzy comprehensive evaluation and the Apriori correlation rule algorithm. The weights were calculated after constructing the physical education course quality index system. The quality of physical education courses in college Z was comprehensively evaluated. It was concluded that teaching explanation and demonstration (0.137), venue equipment (0.133) and physical education class schedule (0.113) had the most significant influence on the quality of physical education courses. The quality of physical education courses in the selected colleges and universities was good, scoring 88.93 points. When the quality of physical education courses is excellent and sound, the confidence level of students’ health status corresponding to excellent and sound is greater than 80%, indicating that physical education courses strongly correlate with students’ health. Among the various indicators of courses analyzed using big data, teaching explanation and demonstration, venue equipment, and students’ health status have stronger correlations.