This study aimed to determine the maxillary and mandibular basal bone regions and explore the three-dimensional positional relationship between the dentition and basal bone regions in patients with skeletal Class I and Class II malocclusions with mandibular retrusion. Eighty patients (40 each with Class I and Class II malocclusion) were enrolled. Maxillary and mandibular basal bone regions were determined using cone-beam computed tomography images. To measure the relationship between the dentition and basal bone region, the root position and root inclination were calculated using the coordinates of specific fixed points by a computer program written in Python. In the Class II group, the mandibular anterior teeth inclined more labially (P < 0.05), with their apices positioned closer to the external boundary. The apex of the maxillary anterior root was positioned closer to the external boundary in both groups. Considering the molar region, the maxillary first molars tended to be more lingually inclined in females (P = 0.037), whereas the mandibular first molars were significantly more labially inclined in the Class II group (P < 0.05). Mandibular anterior teeth in Class II malocclusion exhibit a compensatory labial inclination trend with the crown and apex relative to the basal bone region when mandibular retrusion occurs. Moreover, as the root apices of the maxillary anterior teeth are much closer to the labial side in Class I and Class II malocclusion, the range of movement at the root apex should be limited to avoid extensive labial movement.