To evaluate the three-dimensional (3D) angular displacement (Roll, Yaw, and Pitch) of the upper cervical vertebrae (C1, C2, and C3) in patients with severe mandibular deviation (MD) due to condylar hyperplasia (CH), utilizing a computed tomography (CT)-based segmentation approach. Methods: This retrospective cross-sectional study included 50 patients with MD ≥6 mm caused by hemimandibular elongation (HE) or hybrid form (HF) of CH. The skull, mandible, and cervical vertebrae (C1-C3) were segmented using 3D Slicer software. Angular deviations (Pitch, Yaw, Roll) were measured relative to the Frankfurt plane. Patients were categorized by the side of CH (right or left), and intergroup comparisons were performed using Kruskal-Wallis and Mann-Whitney U tests. Spearman correlation analyses assessed associations between MD magnitude and cervical angles. Results: CH was significantly more prevalent in females (58%; p = 0.021). C2 and C3 exhibited significantly increased lateral Roll inclination toward the side of deviation (p = 0.006 and p = 0.045, respectively). C2 Pitch negatively correlated with MD severity bilaterally (r ≈−0.51, p = 0.02 right; r ≈−0.50, p = 0.02 left). Strong intra-vertebral correlations between Pitch and Yaw were observed in C1 and C2, indicating synchronized vertical and rotational motion. No significant intergroup differences were found in Yaw angles (p > 0.05). Conclusion: Patients with CH and severe MD exhibit consistent patterns of 3D cervical displacement, particularly in lateral inclination and vertical movement, suggesting compensatory postural adaptations in the upper cervical spine.