Background <p>The school physical education program is an important factor in improving students’ physical fitness. In China, secondary school students’ physical fitness is facing a lot of problems, and in order to improve students’ physical fitness, the quality of the implementation of the physical education program by the school should be ensured, so it is necessary to investigate the current status of the implementation of the physical education program by junior high school schools in China, and to analyze the dimensions in which schools with high levels of implementation are better than others, so as to provide a reference for other levels of implementation to better improve the physical fitness of students.</p> Methods <p>A questionnaire was used to assess the physical education implementation levels of 47 schools in the city, covering 10 dimensions. ANOVA was used to compare the differences in the dimensions among schools of different levels, and multiple linear regression analysis was used to explore the influence of each dimension on the implementation level.</p> Results <p>The implementation level of physical education in junior high schools in the city was characterized by a distribution with more in the middle and less at the ends, and the high-level schools were significantly better than the low-level schools in several dimensions. Regression analysis showed that only campus physical activities (β = 0.058, t = 2.616, <i>p</i> = 0.013) and teacher team (β = 0.080, t = 3.331, <i>p</i> = 0.002) had a significant positive predictive effect on the implementation level.</p> Conclusion <p>campus physical activities and teacher team development are the key players in improving the implementation level of physical education. It is recommended that education departments prioritize the strengthening of these two aspects, while paying attention to inter-school differences and promoting the balanced development of regional physical education.</p>