BACKGROUND:: Compared with traditional methods, atlantoaxial pedicle screw internal fixation by three-dimensional (3D) CT reconstruction can improve the accuracy rate and decrease the complication of the pedicle screw internal fixation. OBJECTIVE:: To investigate the treatment method of atlantoaxial instability with the atlantoaxial pedicle screw fixation, with the reference of 3D CT reconstruction of atlas and epistropheus, and to identify its operational directive significance and clinical treatment effects. METHODS:: A total of 30 patients with atlantoaxial instability caused by trauma were recruited, 3D CT reconstructions of atlas and epistropheus were performed before atlantoaxial pedicle screw internal fixation. RESULTS AND CONCLUTION:: No statistical significance was found between actual and designed inclination angle of entrance path and distance between midline and the entrance point for C1 and C2 pedicle screw. The intraoperative anatomical morphology of C1 posterior arch and C2 vertebral arch was consistent with pre-operative CT volume reconstruction images. Pedicle screw internal fixation based on pre-operative CT reconstruction is safe, accurate and effective with few complications and lower X-ray radiation.(Figure is included in full-text article.)