Objective To investigate the differences in rotation trends of maxillary complex through planting mini-implants in different maxillary positions for the protraction of craniofacial suture, so as to provide reference and basis for the appropriate implantation location in clinical orthodontics. Methods The 3D finite element model of the maxillary complex with mini-implant assisted maxillary protraction was established, and the mini-implants were planted in maxillary infrazygomatic crest and the anterior region (6 mm above the root of bilateral incisors and canine), respectively. Traction force of 500 g was applied to analyze the differences in rotation trend of the maxillary complex at different maxillary positions and in different directions. Results When protracted in maxillary infrazygomatic crest region, the maxilla mainly showed counterclockwise rotation trend. When protracted in anterior region, the maxilla mainly showed clockwise rotation trend. Conclusions Protraction at infrazygomatic crest is more suitable for treating patients with hypodivergent crossbite, while protraction in maxillary anterior region is more suitable for treating patients with hyperdivergent crossbite.