The aim of this study was to clarify the three-dimensional changes in maxillofacial morphology following orthognathic surgery using 3D-CT in patients with asymmetrical jaw deformities. The subjects were 30 patients with asymmetrical jaw deformities. Three-dimensional images taken preoperatively and 6months postoperatively were re-aligned using image processing software with the horizontal plane, coronal plane, and midsagittal plane as reference axes. Thirty-nine measurements including 28 distances, nine angles, and two volumes were recorded, and differences between preoperative and postoperative measurements and percentage differences between paired measurements on the deviated and unevolved sides were calculated. Translational and rotational movements of the maxillary dentition and mandibular body and the mandibular ramus internally rotating contributed to improved symmetry of the maxillofacial morphology, but the degree and proportion of these changes varied from case to case and mild asymmetry remained even after surgery. 3D-CT analysis of maxillofacial morphology is essential to accurately evaluate the asymmetry of hard and soft tissue morphology in the maxillofacial region and the degree of improvement after orthognathic surgery, and the tooth movement during preoperative orthodontic treatment should be determined taking into account the movement of the upper and lower jaws during orthognathic surgery.