The invention provides a student physical health data appreciation evaluation method and system. The method comprises the steps of obtaining student physical health data of a current year and student physical health data of a historical year in a target area; calculating score structure increment, average score increment, exercise intervention increment and credible index increment of the physical health data of the students in the target area according to the physical health data of the students in the current year and the historical year; and calculating a comprehensive value-added score of the physical health data of the students in the target area, and performing value-added evaluation on the physical health data of the students in the target area according to the comprehensive value-added score. The physical health data of the students can be fully applied, targeted physical activities and physical training can be carried out in the middle and primary schools according to the corresponding value-added evaluation results, the students are enabled to improve the physical fitness, the strength quality of the students is improved, and the obesity rate and the overweight rate of the middle and primary schools are further controlled.