Objective Through a three-dimensional finite element method study, this research analyzes the effects of different traction sites and directions on the maxilla and upper dentition when using clear aligners combined with protraction, aiming to guide clinicians in scientifically selecting traction sites and directions when applying clear aligners combined with protraction for the treatment of skeletal Class III malocclusion. Methods Finite element models of the zygomaticomaxillary complex, maxillary dentition, and clear aligners were constructed. The models were divided into Group G1 (traction hook at the distal of lateral incisor) and Group G2 (traction hook at the distal of canine). Each group was analyzed under four loading conditions with protraction angles of 0°, 10°, 20°, and 30° relative to the occlusal plane. A unilateral protraction force of 500g was applied. The stress distribution and displacement of maxillary bone and dentition were analyzed. Results 1. When the protraction angle was 30°, both groups showed forward and downward displacement of the maxilla, while other angles resulted in counterclockwise rotation. Under the same protraction direction, Group G2 showed greater displacement than Group G1(total displacement: G1-30° : 0.0073mm; G2-30：0.0093mm). 2. The upper central incisors in Group G1 showed lingual displacement tendency, which increased with the protraction angle. The maxillary dentition in Group G2 showed forward displacement, with minimum total and sagittal displacement at 30° (G2-30° total displacement: 0.026mm, sagittal displacement: -0.0245mm). 3. Stress concentration was mainly observed in the zygomaticomaxillary suture and anterior alveolar bone regions in both groups, decreasing as the protraction angle increased. Conclusions Clear aligners combined with protraction can be applied to skeletal Class III patients with mild maxillary deficiency. When the protraction point is located at the distal of canine with a 30° downward and forward angle to the occlusal plane, the maxilla shows forward and downward displacement with minimal labial movement of upper anterior teeth.