The development of physical education and health courses is not only an important element in the current stage of college education, but also a crucial measure to enhance students’ physical fitness and health. For this reason, this paper is based on intelligent data analysis to build a system to research changes in students’ physical fitness. This paper first analyzes the user and functional requirements for a physical fitness analysis. The clustering algorithm is studied, as is a system for analyzing student body mass, consisting of a browser, a server, and a numerical student body mass testing instrument. Finally, an intelligent analysis of the physical education and health curriculum is carried out using the system. From the empirical analysis, it can be seen that the value of the regression coefficient of physical education and health curriculum is 0.150 (P < 0.001), and the physical education and health curriculum has a significant positive impact relationship on students’ physical fitness, and the percentage of school support mediation effect is 24.52%. In addition, students’ speed, endurance, explosive strength, and power improved with the increase in physical fitness education and grade level. A significant correlation exists between the comprehensiveness and organization of the physical fitness curriculum, with a correlation coefficient of 0.285. Meanwhile, the mean value of the overall evaluation of the system in this paper is 1.452, and it is excellent in terms of simple use, with a mean value as high as 1.475. The synthesis shows that the construction of the physical fitness system in this paper is able to effectively analyze the data of physical education and health courses, improve the physical fitness of the students, and promote the healthy development of students.