Background Clear aligner (CA) treatment has been gaining popularity, but the biomechanical effects of CAs in bimaxillary dentition have not been thoroughly investigated. Direct and indirect strong anchorages are two common anchorage control methods, but the underlying biomechanical mechanism has not yet been elucidated. This study aimed to investigate the different biomechanical effects of CAs in closing the bimaxillary space under different anchorage controls, further instructing the compensation strategies design and strong anchorage choice in clinical practice. Methods Three-dimensional (3D) bimaxillary models of different anchorage controls were created based on cone-beam computed tomography and intraoral scan data. Four first premolars were extracted using 3D modeling software. Finite element analysis was conducted to simulate the space closure process of the CAs. Results In the two strong anchorage groups, the bimaxillary dentition presented different movement patterns during the space closure process, and the lower dentition was more vulnerable to elastic force. From the vertical view, direct strong anchorage with elastic force had the advantage of flattening the longitudinal occlusal curve and resisting the roller-coaster effects, whereas indirect strong anchorage could lead to a deep longitudinal occlusal curve. From the sagittal view, indirect strong anchorage with metallic ligaments had a greater instantaneous anchorage protection effect, particularly in the lower dentition, which reduced the mesial movement of the posterior teeth by nearly four times that of the direct anchorage group. In addition, indirect strong anchorage presented better anterior teeth torque/tipping control, while direct strong anchorage could aggravate lingual tipping of the upper central incisors. Due to the differences in anterior–posterior anchorage and arch shape, compared with the upper dentition, anchorage preservation and vertical control effects were amplified in the lower dentition. Conclusions The biomechanical effects of CAs differed between the two strong anchorage groups. Due to the differences in dentition morphology, anterior–posterior anchorage, and dental arch shape, CAs present different biomechanical effects in bimaxillary space closure. Orthodontists should consider the corresponding mechanical compensation according to specific anchorage control methods and dentitions.

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