Objective To compare biomechanical properties of cortical bone trajectory (CBT) screw and traditional trajectory screw for fixing upper-middle thoracic spine. Methods The tomography images were obtained by CT scanning of normal T7 and T8 segments, and the three-dimensional (3D) model of T7-8 was reconstructed by Mimics software. The finite element model of upper-middle thoracic spine was established by optimizing FreeForm model and pre-processing function of ANSYS software. On this basis, the CBT screw and pedicle screw fixation models after discectomy were established, and 5 N·m flexion, extension, lateral bending and rotation loads were applied to the two model groups, respectively. The displacement and peak stress of vertebrae and implants under different working conditions were compared and analyzed. Results Under different loading conditions, the maximum displacement of CBT screw group was lower than that of pedicle screw group, and the range of motion of CBT screw group was lower than that of pedicle screw group. The stress level of both models was close, and the stress of CBT screw group was slightly lower than that of pedicle screw group. Under the load of flexion, extension and rotation, the maximum vertebral stress of pedicle screw group decreased by 31%, 17% and 18% compared with that of CBT screw group, and under lateral bending load, the vertebral stress of CBT screw group was 20% lower than that of pedicle screw group. Under the load of flexion and rotation, the maximum stress of pedicle screw group decreased by 2% and 11%; however, the maximum stress of CBT screw group was 11% and 1% lower than that of pedicle screw group. Conclusions The stability of CBT screw was better than that of pedicle screw, and the overall stress distribution was similar to that of pedicle screw. However, the vertebral stress distribution of CBT group was slightly inferior. The research findings provide a theoretical basis for the clinical application of cortical screw fixation after the failure in pedicle screw fixation for the upper-middle thoracic vertebrae.