Objective To investigate the feasibility of MRI three-dimensional (3D) reconstruction model in quantifying glenoid bone defect by comparing with CT 3D reconstruction model measurement. Methods Forty patients with shoulder anterior dislocation who met the selection criteria between December 2021 and December 2022 were admitted as study participants. There were 34 males and 6 females with an average age of 24.8 years (range, 19-32 years). The injury caused by sports injury in 29 cases and collision injury in 6 cases, and 5 cases had no obvious inducement. The time from injury to admission ranged from 4 to 72 months (mean, 28.5 months). CT and MRI were performed on the patients’ shoulder joints, and a semi-automatic segmentation of the images was done with 3D slicer software to construct a glenoid model. The length of the glenoid bone defect was measured on the models by 2 physicians. The intra-group correlation coefficient (ICC) was used to evaluate the consistency between the 2 physicians, and Bland-Altman plots were constructed to evaluate the consistency between the 2 methods. Results The length of the glenoid bone defects measured on MRI 3D reconstruction model was (3.83±1.36) mm/4.00 (0.58, 6.13) mm for physician 1 and (3.91±1.20) mm/3.86 (1.39, 5.96) mm for physician 2. The length of the glenoid bone defects measured on CT 3D reconstruction model was (3.81±1.38) mm/3.80 (0.60, 6.02) mm for physician 1 and (3.99±1.19) mm/4.00 (1.68, 6.38) mm for physician 2. ICC and Bland-Altman plot analysis showed good consistency. The ICC between the 2 physicians based on MRI and CT 3D reconstruction model measurements were 0.73 [95%CI (0.54, 0.85)] and 0.80 [95%CI (0.65, 0.89)], respectively. The 95%CI of the difference between the two measurements of physicians 1 and 2 were (–0.46, 0.49) and (–0.68, 0.53), respectively. Conclusion The measurement of glenoid bone defect based on MRI 3D reconstruction model is consistent with that based on CT 3D reconstruction model. MRI can be used instead of CT to measure glenoid bone defects in clinic, and the soft tissue of shoulder joint can be observed comprehensively while reducing radiation.