In recent years, adolescent physical training has received more and more attention, but the risk of sports injury has also increased. Sports injuries not only affect adolescents’ physical health and exercise performance but may also negatively affect their psychological development and social adaptation. Therefore, identifying and understanding the key elements of motor impairment in adolescent physical training is essential for developing effective prevention strategies. However, the occurrence of motor injury is often the result of multiple factors, and there may be complex interactive relationships between factors. To more comprehensively reveal the genetic mechanism of motor injury, the fuzzy set qualitative comparative analysis (fsQCA) method was introduced in this study. An fsQCA is a comparative analysis method based on set theory and Boolean algebra that handles small and medium sample data and identifies multiple combinations of factors (configurations) that lead to the outcome variables. The purpose of this study is to use the fsQCA method to explore the key factors of sports injury and their combined pathways in adolescent physical training to provide a theoretical basis and practical guidance for the development of targeted sports injury prevention strategies.