BackgroundTo investigate changes in the three-dimensional (3D) spatial morphology of the temporomandibular joint (TMJ) and condyle position in adult patients with Class II division 2 malocclusion using a 3D spatial measurement method and to investigate the similarities and differences in the effects of fixed appliance and clear aligner treatments on the TMJ.MethodsCone-beam computed tomography (CBCT) data of 47 adult patients with Class II division 2 malocclusion (25, fixed appliance group; 22, clear aligner group) were collected before and after treatment. Mimics 21.0 was used to reconstruct the TMJ 3D model. Fourteen measurement items, such as the anterior, upper, and posterior joint spaces, were measured directly on the 3D model and compared.ResultsPost-orthodontic treatment, the shape and position of the condyle changed in adult patients with Class II division 2 malocclusion. Reduction in the anterior joint space and increase in the posterior joint space after orthodontic treatment were significant in both fixed appliance and clear aligner treatments; the condyle moved forward to the center of the fossa. The superior joint space and depth of the glenoid fossa increased after clear aligner treatment, but there was no significant change after fixed appliance treatment.ConclusionsThe condylar shape and position in patients with Class II division 2 malocclusion changed significantly post-treatment, indicating that the condyle undergoes adaptive reconstruction during orthodontic treatment in these patients. These results provide a reference for diagnosis, design of treatment plan, and monitoring of treatment in orthodontic clinics.