This study explores the effectiveness of an optimized multidimensional physical education evaluation system in improving students' physical health. A 12-week experimental intervention was conducted with 478 junior and senior high school students, divided into an experimental group and a control group. The experimental group adopted the multidimensional evaluation system, which emphasized dynamic monitoring, personalized feedback, and targeted interventions, while the control group continued with traditional teaching methods. The results demonstrated that the experimental group achieved significant improvements across 10 core health indicators, including BMI, vital capacity, 50-meter sprint, sit-ups, and sit-and-reach, with substantial gains in core strength, flexibility, and cardiopulmonary function. The system also effectively promoted healthy habits and increased exercise participation, with distinct responses observed across gender and age groups. Males and junior high students showed more pronounced improvements in strength and endurance, while females and senior high students excelled in flexibility and BMI management. These findings highlight the limitations of traditional evaluation methods and underscore the advantages of the multidimensional system in fostering comprehensive health development. The study provides evidence-based recommendations for optimizing physical education teaching strategies and advancing student health development, contributing to the Healthy China 2030 strategic goals.