Objective To study the tooth and periodontal stress distribution and tooth displacement after apical root resection, so as to provide data support for clinicians to perform apical root surgery and improve the cure rate of apical root surgery. Methods Three-dimensional (3D) finite element model of normal maxillary central incisor with its periodontal tissues was established based on Micro CT image data. Then periapical periodontitis and apical root resection surgery were simulated. The model of periapical periodontitis and maxillary central incisor with different apical root resection length (3, 4, 5, 6, 7, 8 mm) and their supporting tissues were established. With the occlusal force applied, the biomechanical behavior of postoperative healing teeth was studied by 3D finite element analysis. The optimal apical resection length was obtained by comparing biomechanical effects of surgical restoration. Results The completely healed model reduced the stress (by 26.8%) and displacement (by 7.3%) compared with the apical periodontitis model. With the increase of apical root resection length, the stress of the teeth neck and periodontal ligament increased by 11.14% and 29.27%, respectively, when the root resection was 8 mm. The stress of the alveolar bone increased by 83.11%. The stress of new apical root at the section increased on the whole compared with the same part of normal tooth. The displacement of the tooth along the long axis also increased. The displacement significantly increased by 18.39% when the resection length was over 5 mm. Conclusions Apical root resection significantly improves the biomechanical properties of refractory apical periodontitis tooth. The recommended resection length was 3-5 mm and the crown-to-root ratio (CRR) should be larger than 0.84.