Objective To investigate the method of modeling, finite element modeling and AnyBody musculoskeletal multi-body dynamics simulation technique analyze the biomechanics of clinical orthopaedic surgery. Methods The AnyBody software was used to establish the musculoskeletal motor model of the individualized upper limbs according to the height, weight and CT data of the volunteers. The flexion motion of the elbow in normal people was simulated, and the muscle force, joint force, torque, constraint condition of the humerus during the flexion movement were derived and used as the boundary conditions of finite element analysis.Then, the 3D reconstruction was conducted in the MIMICS software based on CT data. In the Geomagic Studio software, the humeral curved surface and position coordinate matching were completed, and grid division and material assignment were done in the HyperMesh software. Finally, the 3D reconstruction for finite element model of the humerus was introduced into ABAQUS software. The boundary condition data derived from the AnyBody software were applied and the stress calculation analysis was performed. Results The results of the stress and displacement of the humerus during elbow flexion motion were calculated in the ABAQUS software. The maximum stress and displacement of the humerus were 0.76 MPa and 20 μm when flexion of the elbow joint was about 90°. Conclusions A continuous dynamic analysis of humeral stress and displacement during elbow flexion motion was realized, which was more consistent with the requirements of human physiological anatomy and could provide an efficient analysis platform and a new way for studying clinical orthopedic problems.