Objective · To compare the difference of the first molar and alveolar morphology between the deviated side and non-deviated side in skeletal class Ⅲ patients with mandibular deviation by using cone-beam computed tomography (CBCT) image combined with three-dimensional reconstruction measurement technology. Methods · Fifty-six asymmetric CBCT data were evaluated by Mimics 10.0 and 3-Matic software. Some measures were analyzed by t-test including the buccolingual angle, the mesiodistal angle, crown root ratio of first molar and the thickness of alveolar or cancellous bone. Results · The buccolingual angle and crown root ratio of mandibular first molar were significantly larger on the deviated side than on the non-deviated side (P=0.021, P=0.004). Compared with the non-deviated side, the buccal and total cancellous bone thickness of mandibular first molar were significantly smaller on the deviated side (P=0.043, P=0.048). There was no significant difference in the ratio of buccal and total cancellous bone thickness on mandibular first molar (both P=0.118). The measurements of maxillary first molar and maxillary alveolar bone morphology were not significantly different between two sides (all P>0.05). Conclusion · In skeletal class Ⅲ patients with mandibular deviation, although the buccolingual compensation of first molar is found, the position of first molar in the alveolar bone is symmetrical. The asymmetry of alveolar bone morphology are mainly manifested in the reduction of the buccal and total cancellous bone thickness on the mandibular deviated side.