Abstract Using cone beam computed tomography (CBCT), the present study compared three-dimensional (3D) changes in the pharyngeal airway and surrounding tissues in female skeletal class III patients treated with bimaxillary surgery. Twenty-nine female skeletal class III patients with both maxillary hypoplasia and a mandibular excess underwent bilateral sagittal split ramus osteotomy for mandibular setback combined with Le Fort I osteotomy for maxillary advancement. Volumetric measurements were performed using CBCT scans taken at 1 week presurgery and 6 months post-surgery. The oropharynx volumes and the cross-sectional area behind the soft palate decreased significantly. There was an insignificant change in the volume of the nasopharynx ( P > 0.05). The hyoid bone moved downward and posteriorly after surgery. The morphology of the soft palate also changed dramatically, with an increase in the length and thickness. Negative correlations were found between the pharyngeal airway space and the position of the hyoid bone. The change in morphology of the soft palate was significantly correlated with the changes in hyoid bone position. These 3D results suggest that bimaxillary orthognathic surgery significantly changes the position of the hyoid bone and the soft palate together with a significant decrease in the pharyngeal airway space in the correction of skeletal class III malocclusion.