Background. Anterior cervical discectomy and fusion with instrumentation (ACDFI) have been widely used in the treatment of the degenerative disease or traumatic instability of the cervical spine. This study aimed to investigate the clinical efficacy of the autologous vertebral-filled polyetheretherketone (PEEK) cage in anterior cervical discectomy and fusion with instrumentation (ACDFI).Material and Methods. The clinical data of 368 patients who received ACDFI from September 2015 to September 2020 were retrospectively analyzed. According to the material that filled PEEK cage during the surgery, the patients were divided into two groups, the autologous vertebrate group (n = 185) and the autologous iliac group (n = 183). The operative time, operative blood loss, postoperative complications in two groups were recorded and analyzed. The bone graft fusion and postoperative functional outcomes, including scores of modified Japanese Orthopedic Association score (mJOA), Neck Disability Index (NDI), and visual analog scale (VAS) were compared.Results. Patients were followed-up for 14.04 ± 0.98 months. At a 6-months follow-up, the rate of spinal fusion was 96.29% (178/185) in the vertebral group and 95.94% (176/183) in the iliac group, there was no statistically significant difference between the two groups (P>0.05). The postoperative VAS, mJOA, and NDI scores were not significantly different between two groups during the follow-up (P>0.05). The operative time and blood loss in the vertebral group were significantly less than that of the iliac group (P<0.01). In the iliac group, all patients suffered pain in the iliac donor site, 65 patients suffered numbness, 12 patients had fat liquefaction in donor incision, while all patients in the vertebral group had no postoperative complications. Conclusion. The autologous vertebrae-filled PEEK cage can achieve the same clinical outcome as the autologous iliac, but the autologous vertebrae filled PEEK cage have the advantage of shorter operative time, less intraoperative blood loss, and postoperative complications.