This article aims to explore the application and effects of Functional Movement Screen (FMS) in the design of individualized physical training programs for adolescents. The introduction section introduces FMS as a tool to assess the quality of movement patterns, its current application status in various sports fields, and points out that its application in physical training for adolescents is still an under explored zone. The research method section adopts a quantitative research method to analyze the application of FMS in designing individualized physical training programs and its impact on physical training effects and sports injuries through FMS testing and physical training of 100 adolescent athletes aged between 12-16 years. The results show that the application of FMS testing can effectively improve the movement patterns of adolescent athletes, enhance their physical performance, and reduce the risk of sports injuries. However, there are also some limitations in the study, such as the relatively small sample size and short training duration, which may affect the stability and generalization of the results. The conclusion summarizes that the application of FMS testing in the design of individualized physical training programs for adolescents has positive effects, providing new theoretical and practical guidance for adolescent physical training. However, more research is still needed to further validate these results.