Anterior axis-atlanto-occipital transarticular fixation (AAOF) and anterior atlanto-axial transarticular fixation (AAF) are two common anterior screw fixation techniques after odontoidectomy, but the biomechanical discrepancies between them remain unknown. To investigate the biomechanical properties of craniovertebral junction (CVJ) after odontoidectomy, with AAOF or AAF. A validated finite element model of the intact occipital-cervical spine (from occiput to T1) was modified to investigate biomechanical changes, resulting from odontoidectomy, odontoidectomy with AAOF, and odontoidectomy with AAF. After odontoidectomy, the range of motion (ROM) at C1-C2 increased in all loading directions, and the ROM at the Occiput-C1 elevated by 66.2%, 57.5%, and 41.7% in extension, lateral bending, and torsion, respectively. For fixation models, the ROM at the C1-C2 junction was observably reduced after odontoidectomy with AAOF and odontoidectomy with AAF. In addition, at the Occiput-C1, the ROM of odontoidectomy with AAOF model was notably lower than the normal model in extension (94.9%), flexion (97.6%), lateral bending (91.8%), and torsion (96.4%). But compared with the normal model, in the odontoidectomy with AAF model, the ROM of the Occiput-C1 increased by 52.2%, -0.1%, 92.1%, and 34.2% in extension, lateral bending, and torsion, respectively. Moreover, there were no distinctive differences in the stress at the screw-bone interface or the C2-C3 intervertebral disc between the two fixation systems. AAOF can maintain CVJ stability at the Occiput-C1 after odontoidectomy, but AAF cannot. Thus, for patients with pre-existing atlanto-occipital joint instability, AAOF is more suitable than AAF in the choice of anterior fixation techniques.