The objective of this study was to develop a vertebral artery (VA) classification system that improves risk assessment using a 2D map of the VA position at the craniovertebral junction (CVJ), and to outline surgical strategies for managing anomalous VAs during the posterior atlantoaxial joint release, distraction, and fusion technique in the treatment of basilar invagination (BI) and atlantoaxial instability (AAI).In this retrospective study, 125 patients (mean age 44.1 years) with BI and AAI who underwent surgery between January 2019 and April 2021 using the atlantoaxial joint release, distraction, and fusion technique were included. A distribution map was used to better delineate the course of VA and its relationship with the atlantoaxial facet. Under the concept of the current technique, the morphology of VA was reclassified according to the severity of anomaly and surgical risk. Intraoperative risks were graded, and different strategies for handling anomalous vessels were discussed based on the classification.A system of mapping VA distribution was proposed and showed that up to 27% of VAs coursed posterior to the atlantoaxial facet joint, which evidently hampered the facet joint release and manipulation. The VAs coursed in the inferomedial field less frequently. Based on the surgical risk of the posterior atlantoaxial joint release, distraction, and fusion technique, the morphology of VA was classified into 5 types. Additionally, patients were categorized into low-risk, medium-risk, high-risk, and contraindicated groups, according to bilateral VA patterns and institutional surgical experience. Different intraoperative strategies for handling anomalous vessels were introduced and discussed. Intragenic VA injury occurred in 2 of 125 patients (1.6%).The authors introduced a novel method of describing the VA course at the CVJ, called VA mapping, and a VA classification system was proposed to enhance the understanding of risk evaluation in the context of atlantoaxial joint release, distraction, and fusion. A risk stratification system was determined based on bilateral VA patterns, and specific surgical strategies were formulated. The overall iatrogenic VA injury rate was 1.6%, indicating the proposed classification and surgical protocol are reliable and reproducible for minimizing the risk of intraoperative VA injury.