Background: This study aimed to evaluate the effect of craniofacial structure on maxillary airway morphology with skeletal Class I, II and III malocclusions using lateral cephalometric radiographs and cone beam computed tomography (CBCT) in Vietnamese children. Methods: This was a cross-sectional study conducted between June 2023 and June 2024. Study participants included 105 children (14–18 years old, 50 males and 55 females) with a body mass index of 18–25 kg/m2, no history of orthodontic treatment or orthognathic surgery, and no history of cleft lip or palate treatments. Lateral cephalometric radiographs and CBCT were used to identify differences in airway dimensions and respiratory function and assess correlations between craniofacial structure and maxilla airway morphology. Results: The study found a decrease in mandibular length in skeletal groups with CI CII and CIII malocclusion, but significant differences were observed between skeletal CI and CII and between skeletal CII and skeletal CIII. CIII had the largest airway width, followed by CI and CII. The pharyngeal airway volume on CBCT radiographs showed a negative relationship between airway parameters on lateral cephalometric radiographs and airway volume on CBCT radiographs. The Angle formed by the A-nasion line and B-nasion line (ANB) and angle formed by the SN line and GoGn line (SN-GoGn) angles, the angle between the Frankfort plane and mandibular plane (FMA) and the Y-axis showed a positive correlation with mandibular body length, the facial axis and the facial angle. There was also a positive correlation between airway parameters on lateral cephalometric radiographs and airway volume on CBCT radiographs. Conclusions: There was a strong correlation between airway volume and skeletal patterns. Airway dimensions were significantly reduced in skeletal Class II malocclusion patients with a high ANB angle, retrognathic mandible and vertical growth pattern. Clinicians should exercise caution when performing mandibular retrusion in skeletal Class II patients to avoid worsening airway obstruction.