At universities and colleges today, physical education is overly regimented and ignores students’ basic health literacy. This study aims to investigate this phenomenon by examining the state of physical education instruction in colleges and universities nowadays using data mining techniques. In order to retrieve information on the essential literacies of health and physical education courses at colleges and universities, the study first builds a data mining framework using data clustering analysis, association rule extraction, and decision tree algorithms. The teaching-coordination-level model of the core literacies of physical education and health courses is established utilizing the entropy power approach, and the development history of physical education is examined. To determine the best teaching technique for integrating the core literacies of physical education and health courses, an experiment was conducted using College A as an example. The findings indicate that following the trial, students in the experimental class had substantial improvements in their physical and health literacy scores, with the exception of physical fitness (P>0.05). In the previous 10 years, the mean value of the coupling coordination was between 0.6683. The integration of the essential literacies of physical education and health courses accounted for more than 90% of the total credit hours earned in the best colleges and universities. In addition to enhancing physical education abilities, the integration of health and physical education curricula with core literacy in colleges and universities supports the general development of students’ health literacy.