This retrospective study used cone-beam computed tomography to investigated the crown-root morphology and alveolar bone structure in incisors region in subjects with closed deep overbite and comparison the difference between gender and age. The CBCT images for 40 subjects (group C) with Angle II division 2 were selected from patients of the HeFei Stomatological Hospital from November 2023 to March 2024.20 individual normal occlusion subjects (group A),20 patients with Angle II division 1(group B) were included. The crown-root ratio of the maxillary and mandibular anterior teeth, crown-root angle and alveolar bone structure were measured on the CBCT images, the data were statistically analyzed. In addition to mandibular lateral incisor, the crown-root ratio of maxillary and mandibular anterior teeth in the Class II division 2 group was higher than that in the individual normal occlusion group and the Class II division 1 (P < 0. 05). The crown-root angle of maxillary anterior teeth in the Class II division 2 group was smaller than that in the individual normal occlusion group and the Class II division 1 (P < 0. 05). The alveolar bone thickness of the maxillary central incisor was comparatively smaller, while the alveolar bone height was relatively higher in the Class II division 2 group. Age and gender were associated with change in root lengths and crown-root angle for the Class II division 2 group (P < 0. 05). Patients with closed deep overbite malocclusion exhibit a significant difference compared to the controls for most measurements. The patients presenting with Class II division 2 malocclusion exhibit excessive inward positioning of the anterior teeth, resulting in evident crown-root angle, a large crown-root ratio, and minimal labial alveolar bone. In order to keep the tooth movement within the safe range of alveolar bone movement, it is necessary to strictly control the torque and use appropriate orthodontic force to reduce the risk of bone fenestration, bone dehiscence, gingival recession and root resorption.