Background: The relationship between respiratory function and craniofacial morphology has garnered significant attention due to its implications for upper airway and stomatognathic development. Nasal breathing plays a key role in craniofacial growth and dental positioning. This study investigated upper airway morphology and volume differences among individuals with class I, II, and III skeletal anomalies. Methods: Ninety orthodontic patients’ CBCT scans were analyzed to assess the oropharynx and hypopharynx volumes. Skeletal diagnosis was established based on the cephalometric analysis. Results: A significant volume change in the oropharynx and pharynx was demonstrated when comparing class II with class III anomalies (p = 0.0414, p = 0.0313). The total volume of the pharynx was increased in class III anomalies. The area of the narrowest part of the pharynx (MIN-CSA) significantly decreased in classes I and II compared to class III (p = 0.0289, p = 0.0003). Patients with Angle class III anomalies exhibited higher values in the narrowest pharyngeal segment. Gender differences were significant in pharyngeal volumes and morphologies across malocclusion classes. Conclusions: The narrowest segment of the pharynx had the highest values in patients with Angle class III. The volume of the oropharynx was found to be greater in patients with Angle class III versus patients with Angle class II.