Background: The frequent association of basilar invagination (BI) makes the understanding of the pathogenesis of Chiari malformation type I (CMI) difficult. The influence of group B type of BI (the BI without obvious atlantoaxial instability) on the skeletal morphology has not been thoroughly studied. The objective of this study is to evaluate the skeletal alterations in the posterior cranial fossa (PCF) of adult CMI cases with and without group B BI. Methods: Fifty-four adult CMI without BI cases (CMI-only group) and 30 adult CMI with group B BI cases (CMI-BI group) were retrospectively studied. Fifty-six adult patients with unruptured intracranial aneurysms were included as the controls. Several linear and angular variables, and the bony volume of the PCF were analyzed based on thin-slice computed tomography data. Results: Morphological analysis revealed a significant difference in several variables from controls compared to CMI-only, and CMI-BI patients. The clivus and occipital bone, shortened and elevated in CMI-only patients, were further flattened in BI-associated CMI patients. Furthermore, although out of the scope for the diagnostic threshold of BI, the CMI-only cases also had a tendency to form BI. The association of BI modified several variables, without further reducing the bony PCF volume. Conclusions: These findings indicate that the variables associated with group B BI tend to be a continuum of the same pathological abnormalities that originate from the same pathological alterations in CMI patients.