Objective To evaluate the accuracy of cone beam CT (CBCT) in calculating the volume of the bone defect in alveolar cleft. Methods 14 patients with unilateral alveolar cleft were included in this study. Their image data were collected by CBCT scan and imported in the Mimics 10.01 software. The volume of the bone defect in alveolar cleft was calculated by Mimics 10.01 software. The real bone volumes transplanted during operation were measured by sterile syringes and were compared with preoperative CBCT data. Results The volume of bone defect from CBCT calculation was (2.78±0.70) mL, while the real volume obtained in operation was (2.88±0.70) mL. There was no significant difference between the CBCT data and the real bone defect (P>0.05). The accuracy of CBCT in predicting bone defect volume was (95.09±2.56)%. Conclusion The combination of CBCT data and Mimics software can evaluate the bone defect volume in alveolar cleft accurately.