Objectives: The aim of this study is to assess tongue volume (TV), oral cavity proper volume (OCPV), oral cavity volume (OCV), the TV/OCV ratio, pharyngeal airway volume (PAV), nasopharyngeal airway volume (NPAV), and oropharyngeal airway volume (OPAV) in individuals with different sagittal skeletal patterns using cone-beam computed tomography (CBCT), and to explore the interrelationships among these parameters. In addition, this study aimed to enhance the understanding of functional craniofacial anatomy and to support comprehensive planning in both orthodontic and orthognathic treatments. Methods: In all, CBCT images of 165 individuals (88 females, 77 males) were retrospectively selected. The mean age was 21.6 ± 4.5 years (range 17–36 years). The individuals were classified into class I, II, and III based on the sagittal skeletal pattern using the ANB angle. The SNA and SNB angles were also measured. To ensure measurement standardization, all CBCT images were reoriented and resampled to a uniform voxel size of 0.32 mm3 using the “Resample scalar volume” module. Measurements of TV, OCPV, OCV, PAV, NPAV, and OPAV were determined using a semi-automatic segmentation method in the 3D Slicer 5.2.2 software (Surgical Planning Lab, Harvard Medical School, Boston, MA, USA), with different thresholds for air (−1000 to −500) and tongue (−500 to +250). Manual corrections and Gaussian smoothing (1 mm) were applied for tongue segmentation. Group comparisons were made with the Kruskal–Wallis test, followed by post hoc pairwise analysis for significant differences. Spearman’s correlation analysis was used to examine relationships between parameters, and the Mann–Whitney U test assessed gender differences (p < 0.05). Results: SNA, SNB, TV, OCV, and NPAV values were significantly higher in males than in the females (p < 0.05). SNB, TV, and OCV were higher in the class III group compared to class II and I (p < 0.05). A strong positive correlation was identified between TV and OCV (r: 0.907; p < 0.001; p < 0.05), while a negative correlation was found between TV and OCPV (r: −0.435; p < 0.001; p < 0.05). In class II patients, the TV and TV/OCV ratio correlated positively with NPAV, while in class III patients, the TV/OCV ratio correlated negatively with PAV and OPAV (p < 0.05). The SNB value showed a positive correlation with TV, OCV, PAV, and OPAV (p < 0.05). Additionally, the SNA value exhibited a positive correlation with TV and a negative correlation with OCPV (p < 0.05). Conclusion: The relationships between the tongue, oral cavity, and upper airway differed by gender, skeletal patterns, and the relative positions of the mandible and maxilla.