Basilar invagination (BI) is a common deformity. This study aimed to quantitatively evaluate the height of clivus and atlanto-occipital lateral mass (LM) in patients with BI with or without atlas occipitalization (AOZ). We evaluated 166 images of patients with BI and of controls. Seventy-one participants were control subjects (group A), 68 had BI with AOZ (group B), and 27 had BI without AOZ (group C). Parameters were defined and measured for comparisons across the groups. Multiple linear regression analysis was used to test the relationship between Chamberlain's line violation (CLV) and the clivus height ratio or atlanto-occipital LM height. Based on the degree of AOZ, the lateral masses in group B were classified as follows: segmentation, incomplete AOZ, complete AOZ. From groups A to C, there was a decreasing trend in the clivus height and clivus height ratio. There was a linear negative correlation between the clivus height ratio and CLV in the three groups. Generally, the atlanto-occipital LM height followed the order of group B < group C < group A. The atlanto-occipital LM height was included only in the equations of groups B. There were no cases of atlantoaxial dislocation (AAD) in group C. There was a decreasing trend in LM height from the segmentation type to the complete AOZ type in group B. BI can be divided into three categories: AOZ causes LM height loss; Clivus height loss; Both clivus and LM height loss. The clivus height ratio was found to play a decisive role in both controls and BI group, while the atlanto-occipital LM height loss caused by AOZ could be a secondary factor in patients with BI and AOZ. AOZ may be a necessary factor for AAD in patients with congenital BI. The degree of AOZ is associated with LM height in group B.