Objective: To investigate the mechanical effects during en-mass retraction of maxillary anterior teeth with clear aligner using three-dimensional finite element method. Methods: Cone-beam CT (CBCT) was used to scan a female orthodontic patient (26 years old, from Department of Orthodontics, Stomatological Hospital of Chongqing Medical University) whose maxillary first premolars were extracted and maxillary dentition had been aligned and leveled. A finite element model including maxillary teeth-periodontal ligament (PDL)-alveolar bone-clear aligner was established by using Mimics 17.0, SolidWorks 2016 and Geomagic Studio 2015 software packages. The process of 0.2 mm en-mass retraction of anterior teeth using clear aligner was simulated by using non-linear contact method of Abaqus 6.14. The trend and displacement of maxillary teeth, the stress distribution of PDL and alveolar fossae, and the deformation trend of clear aligner were obtained and analyzed. Results: Under the experimental condition, lingual crown tipping and distal tipping movement of anterior teeth were observed, and all of them had the tendency of overbite increasing.The maximum displacement of the central incisor, lateral incisor and canine were 25.16, 50.34 and 24.98 μm, respectively. Meanwhile, the second premolar, first molar and second molar had the tendency of mesial tipping movement, and the maximum displacement of them were 33.04, 2.90 and 16.63 μm, respectively. The stress distribution both at the PDL and alveolar fossae were consistent with tooth movement pattern. It was noted that the stress in the PDL of the canine and second premolar were comparatively big, and the corresponding apical areas of alveolar fossae appeared stress concentration. Concurrently, it was found that the clear aligner showed stress concentration at the junction of adjacent teeth with a tendency of crown directional dislocation. Conclusions During en-mass retraction of anterior teeth with clear aligner, attention should be paid to the overbite and torque in anterior teeth, and the anchorage protection of posterior teeth. At the same time, we should be careful of root resorption of the teeth on both sides of the extraction space.