Research has indicated that modifying shoes’ longitudinal bending stiffness (LBS) could potentially influence running biomechanics and performance among amateur runners. Nevertheless, scant attention has been given to adolescent runners in previous studies, leaving the impact of various LBS shoes on distal joint kinematics and muscular mechanics unclear. Given the distinctive musculoskeletal attributes of adolescents, delving into this matter holds significant importance. Thirteen adolescent amateur runners with rear foot strikes were recruited for the study. Each participant performed running tasks along a 10-meter runway at a speed of 3.3±5% m/s while wearing two types of LBS shoes, randomized for each trial. The specific LBS values of the shoes were 2.7 Nm/rad (low) and 8.6 Nm/rad (high). Lower limb joint biomechanical data were collected using a Vicon motion analysis system and AMTI force platform. Lower limb joint kinematics and muscular mechanics were analyzed using Opensim software. Paired t-tests were employed to identify differences in distal joint kinematics and muscular mechanics during stance phases. We found that there was a significant increase in contact time, while the range of motion (ROM) of the metatarsophalangeal (MTP) joint in the sagittal plane significantly decreased in the high LBS shoe condition. Additionally, the impulse of flexor digitorum brevis and flexor hallucis longus significantly increased under the high LBS shoe condition. The results show that high LBS shoes impose a greater load on the distal muscles, potentially elevating the risk of running-related injuries. The low LBS shoes are more suitable for adolescent runners.