C1 transpedicular screw (C1TS) placement provided satisfactory pullout resistance and 3D stability, but its application might be limited in patients with basilar invagination (BI) due to the high incidences of the atlas anomaly and vertebral artery (VA) variation. However, no study has explored the classifications of C1 posterior arch variations and investigated their indications and ideal insertion trajectories for C1TS in BI. To investigate the bony and surrounding arterial characteristics of the atlas, classify posterior arch variations, identify indications for C1TS, evaluate ideal insertion trajectories for C1TS in BI patients without atlas occipitalization (AO), and compare them with those without BI and AO as control. A total of 130 non-AO patients with and without BI (52 patients and 78 patients, respectively) from two medical centers were included at a 1:1.5 ratio. The posterior arch variations were assessed using a modified C1 morphological classification. Comparisons regarding the bony and surrounding arterial characteristics, morphological classification distributions, and ideal insertion trajectories between BI and control groups were performed. The subgroup analyses based on different morphological classifications were also conducted. In addition, the factors possibly affecting the insertion parameters were investigated using multiple linear regression analyses. The BI group was associated with significantly smaller lateral mass height and width, sagittal length of posterior arch, pedicle height, vertical height of posterior arch, and distance between VA and VA groove (VAG) than control group. Four types of posterior arch variations with indications for different screw placement techniques were classified; Classifications I and II were suitable for C1TS. The BI cohort showed a significantly lower rate of Classification I than the control cohort. In the BI group, the subgroup of Classification I had significantly larger distance between the insertion point (IP) and inferior aspect of the posterior arch. In addition, it had the narrowest width along ideal screw trajectory, but a significantly more lateral ideal mediolateral angle than the subgroup of Classification II. Multiple linear regression indicated that the cephalad angle was significantly associated with the diagnosis of BI (B = 3.708, P < 0.001) and sagittal diameter of C1 (B = 3.417, P = 0.027); the ideal mediolateral angle was significantly associated with BMI (B = 0.264, P = 0.031), sagittal diameter of C1 (B = - 4.559, P = 0.002), and pedicle height (B = - 2.317, P < 0.001); the distance between the IP and inferior aspects of posterior arch was significantly associated with age (B = - 0.002, P = 0.035), BMI (B = - 0.007, P = 0.028), sagittal length of posterior arch (B = - 0.187, P = 0.032), pedicle height (B = - 0.392, P < 0.001), and middle and lower parts of posterior arch (B = 0.862, P < 0.001). The incidence of posterior arch variation in BI patients without AO was remarkably higher than that in control patients. The insertion parameters of posterior screws were different between the morphological classification types in BI and control groups. The distance between VA V3 segments and VAG in BI cohort was substantially smaller than that in control cohort. Preoperative individual 3D computed tomography (CT), CT angiography and intraoperative navigation are recommended for BI patients receiving posterior screw placement.