Background: The persistence of college students’ physical exercise behavior has an important impact on their physical health level and their positive psychological effects. The health behavior ecology model is more comprehensive and progressive than other exercise psychology theories in explaining the effect of physical activity intervention on long-term maintenance. Based on this, In this study, using the socio-ecological model theory as the entry point, applying five different levels of influencing factors in the theoretical model to the field of adolescent physical exercise behavior, The aim is to seek the internal connection between the ecological factors that promote college students’ physical exercise behavior through the investigation, so as to provide corresponding intervention strategies for promoting the healthy development of their physical fitness. So as to promote the formation of college students’ physical exercise habits. Methods: In 2023, 1015 college students were surveyed by questionnaire and measurement scale, followed by descriptive statistical analysis of college students’ current physical exercise behavior, and factor analysis of ecological factors affecting college students’ physical exercise. Results: From the behavior characteristics of college students’ physical exercise, different gender of college students in physical exercise, weekly exercise, exercise time is very significant difference (P < 0.001), the boys in sports participation higher than girls 15.2%, choose occasionally exercise boy’s ratio 10% higher than girls, girls do not participate in exercise more than boys. In terms of exercise time, a few boys choose to do physical exercise on weekends; the proportion of boys in more than 60 min of physical exercise is 7 percentage points higher than girls. In the time of extracurricular exercise, support of parents and physical exercise (P < 0.05), there was no significant difference between male and female students in the aspects of intensity of each exercise, participation in sports competition and reasons for not exercise (P > 0.05). The principal component analysis of the influencing factors of college students’ physical exercise behavior was conducted from the individual, family, school, community, and policy levels. The KOM value was 0.984, which met the judgment criteria of factor analysis. Through principal component analysis of the above five levels, according to the requirements of factors greater than 1, the individual level, family level, school level and policy level respectively two factors, corresponding cumulative contribution rate is 56.545%, 595.350%, 64.870% and 85.700% respectively, community level three factors, corresponding to the cumulative contribution rate of 76.450%. Conclusion: The advantage of the health behavior ecology model is that the comprehensive intervention strategies based on multi-level, multi-level effects greatly expand people’s understanding of the intervention. This model is applied to the field of physical health promotion of college students, to study human exercise behavior through the joint action of physiological, psychological and environmental factors, so as to more comprehensively reveal the various factors of exercise behavior, as well as the mutual relationship and influence between them. The results of this study indicate that: among the ecological factors that affect the physical exercise behavior of college students, the individual factors of college students are a necessary condition for physical exercise, while family, school and community factors affect the direction of the change and development of college students’ physical exercise behavior. Policy factors are a powerful driving force for college students’ physical exercise behavior. Only by considering the relationship between the relevant factors can we better understand the characteristics of college students’ physical exercise development, put forward the corresponding intervention strategies, and promote the formation of college students’ physical exercise habits through effective ways.