Objective To compare the differences in lower limb joint kinematics and muscle activation between Asian squat (AS) and Western squat (WS). Methods Eleven healthy adults were recruited to complete the biomechanical test of AS and WS. The 3D motion analysis system, force plates and surface electromyography (EMG) were used to collect kinematics, kinetics and muscle activation data of the subjects during two squats, and muscle force of the lower limb was also calculated by OpenSim. Results AS showed pelvis forward flexion, while WS showed pelvis backward extension at the time of peak knee flexion angle. Compared with the AS, a significant smaller hip flexion, larger knee flexion, larger hip abduction and hip rotation angles were found in WS at the time of peak knee flexion angle. Compared with AS, a significant greater peak force of soleus was found in WS during descent and ascent phases of squat. Additionally, a smaller peak force of anterior tibia was found in WS than that in AS during descent and ascent phases of the squat. No significant differences were found in other muscle peak force and the time of peak force between AS and WS. Conclusions The combined tibialis anterior activation and proximal joint flexion might be beneficial to stabilization during AS. The soleus muscle activation was significant in WS with heel lifting. The muscle activation pattern of proximal joint was similar between AS and WS. This study provides theoretical guidance for the design of clinical squat rehabilitation programs or the selection of squat training.