Objective: To compare the effects of expansion screw with maxillary protractor and clear aligners combined with maxillary protractor on the maxilla and maxillary dentition of mixed dentition patients with class Ⅲ skeletal malocclusion using finite element analysis, further providing clinical guidance for clear aligner treatment. Methods: A finite element model was established based on maxillofacial cone-beam CT data of a 10-year-old boy with mixed dentition, class Ⅲ skeletal malocclusion, who visited Department of Orthodontics, School of Stomatology, The Fourth Military Medical University in January, 2024. The expander with protractor group (group A) and the clear aligners with protractor group (group B) were divided. The arch was extended by 0.25 mm in both groups, and the forward pull force was 2.94 N (working condition 1) and 4.90 N (working condition 2), respectively. The initial displacement trend of maxilla and maxillary dentition in two groups under two working conditions were evaluated. Results: Under two working conditions, the maxilla of both groups showed clockwise rotation and labial inclination. The labial inclination of maxilla was more significant in clear aligners with protractor group, about 2.2-3.0 times that of expander with protractor group under the same working condition. Maxillary dentition showed mesial and buccal displacement, with anterior teeth extrusion and posterior teeth intrusion in two groups under two working conditions. Under the working condition 1 and 2, the labial displacement of central incisor of clear aligners with protractor group (-0.065, -0.089 mm) were greater than that in expander with protractor group (-0.024, -0.024 mm). Under two working conditions, the posterior teeth of expander with protractor group moved close to the buccal bodily direction, while those of clear aligners with protractor group moved tilted towards the buccal direction in the horizontal direction. The forward displacement trend of maxilla and maxillary dentition in clear aligners with protractor group was more obvious than expander with protractor group with the increase of the forward pull force. Under two working conditions, the anterior teeth' s hydrostatic stress of periodontal membrane and the equivalent stress of alveolar bone in clear aligners with protractor group were higher than those in expander with protractor group, mainly concentrated on the labial cervical region of the incisor. Conclusions: Clear aligners combined with maxillary protractor can produce forward force on the maxilla, but labial inclination occurs in the anterior teeth. It can be an effective orthopedic treatment strategy for mixed dentition patients with class Ⅲ skeletal malocclusion.