In view of the current situation of female students’ participation in physical exercise in junior middle schools, taking female students in Bao’an Middle School as an example, the original data of female students’ physical exercise in junior middle schools were obtained through questionnaire survey, and the analytic hierarchy process (AHP) was used for analysis. The research results show that sports venues, time pressure, physical education courses and physical fitness play a leading role in all the factors that affect the physical exercise of junior high school female students, which provides theoretical and practical basis for improving school physical education and guiding junior high school female students to form a sense of physical exercise and a healthy lifestyle.