This research looked back at past events. The purpose was to add to the existing knowledge of cervical sagittal alignment in congenital cervical deformities by presenting a morphological map of cervical sagittal alignment in basilar invagination (BI), a congenital aberration of the craniovertebral junction. Scholars disagree on the best way to achieve cervical sagittal alignment and other surgical goals. Fewer studies have examined cervical spine deformities present at birth, and most studies describe the sagittal alignment of the cervical spine in patients with acquired cervical illnesses or in healthy participants. Radiographs of the cervical spine were taken laterally on 87 people with traumatic brain injury and 98 healthy controls. Inlet parameters for the head, neck, and chest were evaluated. When compared to asymptomatic subjects, patients with BI showed significantly greater values for cranial tilt, cranial incidence angle, the sagittal vertical axis (SVA) CGH-C7, C2-C7 angle, cervical tilt, and considerably smaller values for cranial slope, C0-C2 angle, C0-C7 angle, SVA C2-C7, spine tilt, thoracic inlet angle, and neck tilt. When comparing BI patients with and without fusion (atlanto-occipital assimilation), SVA C2-C7 was the cervical parameter most highly linked with the cranial, cervical spine, and thoracic inlet parameters. Patients with traumatic brain injuries differed from asymptomatic subjects in a statistically meaningful way. There was a reduction in upper cervical lordosis, an increase in lower cervical lordosis, and a reduction in the thoracic inlet angle in those with BI. The SVA C2-C7 is a crucial indicator of cervical sagittal alignment in patients with BI. Alignment of the cervical spine was strongly correlated with cranial alignment, especially thoracic inlet alignment, in both patients with craniovertebral junction abnormalities and the asymptomatic population.