This study aimed to investigate the evaluation of biomechanical changes in articular cartilage in patients after anterior cruciate ligament (ACL) reconstruction by magnetic resonance imaging (MRI) based on a three-dimensional (3D) finite element model. The data of 90 patients undergoing arthroscopic ACL reconstruction in the hospital were collected and divided into the stable group (54 cases) and the unstable group (36 cases). A load of up to 134N was applied to the 3D finite element model, and the kinematics of knee flexion at 0°, 30°, 60°, and 90° were examined. The tibial anteversion, tibial rotation, and ACL/graft tension were recorded in the 3D finite element model, which was randomly divided into the normal group (intact group, n = 30), the ACL rupture group (deficient group, n = 30), and the anatomical reconstruction group (anatomical group, n = 30). When the graft was fixed at 0°, the anterior tibial translation at 30°, 60°, and 90° in the anatomic group was 8–19% higher than the normal value under 134 N anterior load. The tibial internal rotation in the anatomic group was 18% and 28% higher than the normal value at 30° and 90°. When the graft was fixed at 30°, the anterior tibial translation at 60° and 90° of the anatomic group was 15% higher than the normal value. The tibial internal rotation at 90° of the anatomic group was 16% higher than the normal value, and the above differences had statistical significance P < 0.05 . MRI images were used to assess the bone tunnel angle, and the statistical analysis by the independent-samples t-test showed that there were significant differences in the bone tunnel angle between the stable group and the unstable group P < 0.05 . Currently, based on the 3D finite element model, MRI can accurately evaluate the postoperative effect of anatomical ACL reconstruction in the position, diameter, and angle of tibial and femoral bone tunnels, which can be applied to clinical promotion.