Objective To compare the effects of clear-aligner orthodontics with two orthodontic sequences on molar distalization. Methods A finite-element model of seven right mandibular teeth with periodontal alveolar bone and braces was established. Two molar distalization sequences were selected to simulate the distal movement of the second molar (0.5 mm), and the long-term tooth movement was simulated using the alveolar bone reconstruction technique. Results The maximum distal displacement of the second molar with V-pattern and ZC sequences was 0.27 mm and 0.34 mm, respectively, and the ZC distal displacement efficiency was increased by 13.34%. The tooth inclination was corrected by 0.18 mm and 0.44 mm, the lingual inclination was corrected by 1.15° and 2.69°, respectively, and the correction rate of ZC lingual inclination was increased by 15.01%. The distal tilt of the ZC increased by 1.83° and 0.84°, and the distal tilt of the ZC decreased by 54.10%. Conclusions The ZC sequence method can realize distal molar movement more effectively, reduce the distal inclination of the molar, and correct the lingual inclination of the molar, providing favorable conditions for orthodontic treatment of anterior teeth.