Objectives <p>The present study was aimed to assess three-dimensional (3D) quantitative changes of condyle in patients with Class III facial asymmetry after bimaxillary orthognathic surgery.</p> Materials and methods <p>Fifty-five eligible patients with Class III facial asymmetry received Le Fort I osteotomy and bilateral sagittal split osteotomy (BSSO) with or without genioplasty from January 2020 to June 2022 were included. Cone-beam computed tomography (CBCT) for each patient was collected at 3 stages: 1 week preoperatively (T0), immediately after surgery (T1) and at least 12 months postoperatively (T2). Positional changes and bone remodeling of condyles were measured based on voxel- and surface-registrations using ITK-SNAP and 3D Slicer and compared between various stages. Correlations between these changes, mandibular surgical movements and skeletal stability were further explored.</p> Results <p>Most condyles at deviated side (DS) tended to shift inferiorly, anteriorly and to non-deviated side (NDS), while condyles at NDS were displaced posteriorly, inferiorly and laterally from T0 to T1. Condyles showed upward pitch, outward yaw and lateral roll at both sides. Bone resorption was more frequently observed in the posterior area of condylar surface at NDS. Significant correlations were found between mandibular anteroposterior/transverse stability and DS condylar lateral shift or NDS condylar yawing after surgery (T1-T2), respectively.</p> Conclusions <p>Our results comprehensively characterize 3D condylar changes and their associations with skeletal stability after surgical correction of Class III facial asymmetry.</p> Clinical relevance <p>These findings advance current understanding of complex condylar changes after bimaxillary orthognathic surgery in Class III facial asymmetry patients.</p>