Background: This study was to investigate the correlation between changes of the soft and hard tissues three-dimensionally in class III orthognathic patients using cone-beam computed tomography. Methods: Cone-beam computed tomography images were obtained within 2 weeks before surgery and at 6 months after surgery in 18 adult class III patients who underwent Le Fort I osteotomy and bilateral intraoral vertical ramus osteotomy. Subjects were divided into group 1 with no mandibular asymmetry (menton deviation, <2 mm; n = 9) and group 2 with mandibular asymmetry (menton deviation, >4 mm; n = 9). Landmarks were designated on the reconstructed three-dimensional models. Correlations and proportions of changes of the soft tissue to hard tissue were calculated. Results: There were significant correlations of Delta B' to Delta B and Delta Pog' to Delta Pog in both groups on the horizontal axis (P < 0.05), and their proportions were 0.53 and 0.67 in group 1 and 0.77 and 0.88 in group 2, respectively. There were significant correlations of Delta B' to Delta B, Delta Pog' to Delta Pog, and Delta Me' to Delta Me on the sagittal axis in both groups (P < 0.05), and their proportions were 0.94, 0.84, and 0.96 in group 1 and 0.95, 0.91, and 1.03 in group 2, respectively. There were significant correlations of the three-dimensional distances between Delta B' to Delta B, Delta Pog' to Delta Pog, and Delta Me' to Delta Me in both groups (P < 0.05), and their proportions were 0.92, 0.79, and 0.95 in group 1 and 0.92, 0.88, and 0.97 in group 2, respectively. However, there were no significant correlations between changes in soft and hard tissues on the vertical axis in both groups (P > 0.05). Conclusions: In class III orthognathic patients with mandibular asymmetry, the proportions of Delta B' to Delta B, Delta Pog' to Delta Pog, and Delta Me' to Delta Me on the horizontal and sagittal axes and the three-dimensional distances were different from patients with no mandibular asymmetry.