Objectives: This study aimed to determine the three-dimensional (3D) correlation between maxillomandibular complex parameters and pharyngeal airway dimensions in different sagittal and vertical malocclusions. Methods: This retrospective cross-sectional study included the CBCT scans of 368 patients with a mean age of 23.81 ± 3.01 years. The patients were classified into three groups (skeletal Class I, II, and III). Each class group was divided into three subgroups based on vertical growth patterns (hypo-, normo-, and hyperdivergent). The maxillomandibular complex was evaluated in the three planes using 16 skeletal measurements. Naso-, oro-, hypo-, and total pharyngeal airway spaces were assessed in terms of width, volume, surface area, and minimum constricted area (MCA). Two-way ANOVA followed by the Bonferroni post-hoc test were used. Results: The nasopharyngeal airway space was significantly lowest regarding sagittal and lateral widths in the skeletal Class III patients, the lowest volume and surface area were in hyperdivergent patients, and MCA was the highest in Class II and hypodivergent patients. The oro- and hypopharyngeal sagittal width, volume, surface area, and MCA were the lowest in the hyperdivergent patients, and oropharyngeal lateral width and hypopharyngeal sagittal width were the highest in skeletal Class III. The total pharyngeal volume, surface area, and MCA were the lowest in the hyperdivergent patients, and skeletal Class II patients had the lowest MCA. Conclusions: The pharyngeal airway dimensions differ with various sagittal and vertical malocclusions. These differences could apply to diagnosis, treatment planning, and possible changes following orthodontic/orthopedic or surgical treatment.