The aim of this study was to investigate the effect of balance training on the physical motor function of adolescent female football players. Thirty female football players aged 11-12 years were selected from Ausheng Football Club as the study subjects, and they were divided into a test group and a control group of 15 each using experimental testing and mathematical statistics methods. The experimental group received balance training intervention for a period of 5 weeks while the control group did not receive any intervention. The Y-Balance test and FMS test were used as assessment indicators to evaluate the balance and body movement function of the athletes respectively. Differences in performance between the two groups before and after training were compared and the relationship between balance ability and physical motor function was analyzed by methods such as paired samples t-test and independent samples t-test. The results showed that compared with the control group, the experimental group showed significant improvement in all balance indicators, especially in medial back and overall balance. In addition, the experimental group showed significant improvement in hurdle stride, linear lunge, and rotational stability indicators. The overall motor function of the experimental group improved significantly as assessed by the Functional Movement Screen (FMS), which indicated that the balance training was very effective. The Y-balance test further confirmed that the experimental group showed a substantial improvement in balance, while the control group showed little change. In addition, the results of the Y-balance test showed a moderate positive correlation with the results of the FMS test, suggesting a relationship between balance and functional movement. These findings emphasize the positive impact of balance training on the physical motor function of young female footballers, demonstrating the importance of balance training in motor development and injury prevention.