Objective To compare characteristics of stress variations in 3D finite element models of normal and degenerative lumbar vertebrae and the dose-effect relationship, and analyze the mechanism of mechanical balance by traditional Chinese medicine (TCM) manipulation on degenerative lumbar vertebrae. Methods The 3D finite element model of intact, real human degenerative lumbar vertebrae (L4-5) was established to simulate the physiological activity of flexion and extension in lumbar vertebrae. The characteristics of stress variation in degenerative lumbar vertebrae under external loading, namely, the TCM manipulation was analyzed, and the stress variation in degenerative lumbar vertebrae under gradual increasing-external loading was analyzed as well, which was compared with the stress and strain variation in normal lumbar vertebrae under different motion status. Results Under different motion status, the stress distributions on lumbar disc as well as the elastic modulus of nucleus pulposus and fiber ring showed a gradually increasing tendency with lumbar degeneration increasing. TCM manipulation could change the stress distributions on lumbar disc, enlarge the space of spinal canal to a certain degree, and decrease the stress on nerve root. Stresses on small joints of the vertebral body and vertebral pedicle under posterior extension were larger than those under anterior flexion, while stresses on intervertebral disc under anterior flexion were greater than those under posterior extension, which showed a gradually increasing trend from top to bottom. Conclusions The mechanical environment of human lumbar vertebrae can be balanced by TCM manipulation, for the purpose of improving and treating lumbar disc diseases. The comparison with the 3D finite element model of normal human lumbar vertebrae and investigation on lumbar degeneration from perspective of changes in biomechanical environment and characteristics can provide scientific basis for clinic application of TCM manipulation in prevention and treatment of lumbar degenerative diseases, as well as new research idea for studying mechanical mechanism of TCM manipulation in effective prevention and treatment of lumbar lesions.