Muscle atrophy of the residual limb after lower-limb amputation is a disadvantage of amputees' rehabilitation. To investigate the biomechanics mechanism of muscle atrophy of the residual limb, we built a finite element model of a residual limb including muscle, skeletons and main vessels based on magnetic resonance images of a trans-femoral amputee, and studied the biomechanics effects of the socket of the lower-limb prosthesis on the soft tissue and vessels in the residual limb. It was found that the descending branch of the lateral femoral circumflex artery suffered the most serious constriction due to the extrusion, while that of the deep femoral artery was comparatively light. Besides, the degree of the constriction of the descending branch of the lateral femoral circumflex vein, femoral vein and deep femoral vein decreased in turn, and that of the great saphenous vein was serious. The stress-strain in the anterior femoral muscle group were highest, while the stress concentration of the inferior muscle group was observed at the end of the thighbone, and other biomechanical indicators at the inferior region were also high. This study validated that the extrusion of the socket on the vessels could cause muscle atrophy to some degree, and provided theoretical references for learning the mechanism of muscle atrophy in residual limb and its effective preventive measures.