Cable-dragged reduction and cantilever beam internal fixation can provide promising results in the treatment of atlantoaxial dislocation or instability. However, bilateral atlantoaxial joints bone autografting has not been conducted in this technique. We aim to evaluate the safety and effectiveness of bilateral atlantoaxial joints bone autografting in posterior cable-dragged reduction and cantilever-beam internal fixation. In this retrospective study, we included 14 patients with a minimum 24-month follow-up from December 2019 to September 2020. The granular bone harvested from the iliac crest was packed into the bilateral atlantoaxial joints of 14 patients in posterior cable-dragged reduction and cantilever-beam internal fixation. X-ray imaging and cervical computed tomography (CT) were performed during follow-up. The time required for bone fusion was recorded. The clinical outcomes were evaluated using the JOA scores, NDI, and VAS scores. Mann-Whitney U test, the chi-squared test, or the Fisher exact test were used to compare the two groups regarding patient characteristics, clinical outcomes, bone fusion rates, and cervical sagittal alignment. The operations were successfully performed in all patients without any intraoperative complications. The mean operation time was (169.64 ± 20.91) minutes, and the intraoperative blood loss was (130.71 ± 33.62) mL. All patients received satisfactory reductions and firm bony fusion at the final follow-up. The fusion rates were 64.29% in the atlantoaxial joints and 21.43% in post bone graft area at 3 months postoperatively, and a significant difference was observed (p = 0.022). Besides, the cervical sagittal alignment in all patients was well maintained in the last follow-up compared to preoperatively. Importantly, a complete bony fusion in the atlantoaxial joints was observed in all patients. Moreover, the JOA, NDI, and VAS scores had improved significantly at the last follow-up. Bone autografting of the bilateral atlantoaxial joints is a safe and effective technique to increase bone fusion rates, shorten bone fusion time, and reduce complication rates when the cable-dragged reduction and cantilever beam internal fixation approach is used. Therefore, it is a cost-effective surgical procedure for treating patients with atlantoaxial dislocation or instability.