Although many studies have investigated the benefits of multimodal intraoperative monitoring (MIOM) during cervical spine surgery, the benefits of MIOM in craniovertebral junction (CVJ) surgery remain unclear. The objectives of the present study were to report our clinical experience in CVJ surgery with the use of MIOM and to identify risk factors that could affect MIOM changes during surgery of CVJ pathology.We reviewed the MIOM records of 146 patients who had undergone high cervical spinal surgery. The patients were grouped by the MIOM data recorded during surgery; the patients were included in either the MIOM or non-MIOM change group. The analyzed risk factors included demographic, myelopathy, preoperative Japanese Orthopedic Association (JOA) score, spinal cord diameter, and surgical factors. Univariate and multivariate analyses were performed to identify the risk factors for changes in MIOM data during surgery and postoperative neurological deficits.Our results revealed that the incidence of postoperative neurological complications was 4.1% after CVJ surgery; this rate was significantly greater in the MIOM change group than in the non-MIOM change group (21.7% vs. 0.8%; P0.01). Multiple regression analysis revealed that preoperative myelopathy, preoperative JOA score, and congenital anomaly/tumor were independently associated with MIOM changes during surgery.Postoperative neurological complications are not uncommon after CVJ surgery, and the incidence was significantly greater in the MIOM change group. Preoperative myelopathy, preoperative JOA score, and CVJ pathology related to congenital anomaly or tumor were independent risk factors for changes in MIOM data during surgery.