Objective: To analyze the structural types of physical fitness, key discriminating indicators, and their interval characteristics among Chinese junior high school students, so as to provide a reference for classification and identification of school based physical fitness monitoring results. Methods: Based on physical fitness surveillance data collected from October to December in 2021 from 40 206 junior high school students in 27 provinces (autonomous regions and municipalities) of China, cluster analyses were conducted separately by sex to classify physical fitness structural types. A multiclass classification model was constructed to extract key discriminating indicators for different structural typologies, and SHapley Additive exPlanations (SHAP) dependence analysis was further applied to characterize their interval features. Results: Four major structural types were identified in both boys and girls:a type characterized by relatively high cardiopulmonary function (C1) (26.4%，21.0%), a balanced physical fitness type (C2) (33.1%，33.1%), a type characterized by relatively weak overall physical fitness (C3) (16.8%，18.9%), and a type characterized by relatively strong overall physical fitness (C4) (23.7%，27.0%). In boys, the key discriminative indicators were mainly pull ups, body mass index (BMI) and the 1 000 meter run; in girls, they were mainly vital capacity, the 800 meter run, and BMI. Some key indicators showed relatively stable interval boundaries across structural types, such as a 1 000 meter run time of ≥5 min 11 s for type C3 in seventh grade boys and an 800 meter run time of ≥4 min 20 s for type C3 in seventh grade girls. Conclusion Four major physical fitness structural types can be identified among Chinese junior high school students, with sex specific patterns in the key discriminative indicators and their interval characteristics.