In order to solve the limitations of traditional physical education in time and space, this paper explores the development path of physical education informatization in colleges and universities based on the perspective of modern pedagogy. The data results are analyzed and studied by testing the physical fitness of college students in a school, followed by using the physical fitness clustering method as well as constructing the ID3 tree physical fitness early warning model for male and female students. A simple analysis of the students’ physical fitness test yielded that the mean physical fitness score for male students was 70.46 and the mean total score for female students was 73.84, with female students performing better than male students overall. The model analysis shows that there is a phenomenon of “the increase of strength and flexibility” among the university students. There is a significant difference between the changes in test indicators of male and female students. The model of this paper does not need the results of all the test items to judge whether the total score passes or not, and the model can be used to judge the total score of the missing items due to non-participation in a certain program. The experimental data show that this model is very suitable for the development of physical education teaching information in colleges and universities, and plays a good guiding role in improving teaching levels.