The retrospective study examined changes in the root length and alveolar bone surrounding maxillary incisors in patients with skeletal Class III malocclusion treated by surgical orthodontic treatment with either fixed appliances (FAs) or clear aligners (CAs). A total of 60 subjects were divided based on appliance type used. Cone beam computed tomography scans were taken at three stages: before treatment, after presurgical orthodontic treatment, and post-treatment for both groups. Vertical alveolar bone level and horizontal alveolar bone thickness (ABT) were measured at four heights (3, 6, and 9 mm from the cementoenamel junction, and the root apex), along with root length, at these time points. Both groups showed a decrease in root length, with the CA group experiencing a significantly smaller reduction (0.4 ± 0.79 mm) compared with the FA group (0.64 ± 0.8 mm; P = 0.02). The FA group demonstrated more significant reduction in palatal ABT (P < 0.05) and greater root resorption, whereas the CA group exhibited considerable labial marginal bone resorption (P = 0.007) and a notable decrease in labiolingual inclination (P = 0.042). The findings suggest that FA and CA might lead to decreased ABT and significant root resorption, with FA therapy likely resulting in more pronounced effects. Both modalities led to notable vertical bone loss, particularly, on the labial side of the maxillary incisors in the CA group during postsurgical orthodontic treatment. Preventing iatrogenic deterioration of periodontal support surrounding the incisors is crucial during presurgical and postsurgical phases.