Introduction The purpose of this study was to clarify the relationships between upper airway factors (nasal resistance, adenoids, tonsils, and tongue posture) and maxillofacial forms in Class II and III children. Methods Sixty-four subjects (mean age, 9.3 years) with malocclusion were divided into Class II and Class III groups by ANB angles. Nasal resistance was calculated using computational fluid dynamics from cone-beam computed tomography data. Adenoids, tonsils, and tongue posture were evaluated in the cone-beam computed tomography images. The groups were compared using Mann-Whitney U tests and Student t tests. The Spearman rank correlations test assessed the relationships between the upper airway factors and maxillofacial form. Results Nasal resistance of the Class II group was significantly larger than that of the Class III group ( P  = 0.005). Nasal resistance of the Class II group was significantly correlated with inferior tongue posture ( P  <0.001) and negatively correlated with intermolar width ( P  = 0.028). Tonsil size of the Class III group was significantly correlated with anterior tongue posture ( P  <0.001) and mandibular incisor anterior position ( P  = 0.007). Anterior tongue posture of the Class III group was significantly correlated with mandibular protrusion. Conclusions The relationships of upper airway factors differ between Class II and Class III children.