Purpose: To evaluate the accuracy of the imaging reformation of cone beam computed tomography for the assessment of bone defect healing in rat model. Materials and Methods: Sprague-Dawley strain rats weighing about 350 gms were selected. Then critical size bone defects were done at parietal bone with implantation of collagen sponge. The rats were divided into seven groups of 3 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 6 weeks, and 8 weeks. The healing of surgical defect was assessed by multi planar reconstruction (MPR) images and three-dimensional (3-D) images of cone beam computed tomography, compared with soft X-ray radiograph and histopathologic examination. Results: MPR images and 3-D images showed similar reformation of the healing amount at 3 days, 1 week, 2 weeks, and 8 weeks, however, lower reformation at 3 weeks, 4 weeks, and 6 weeks. According to imaging-based methodologies, MPR image revealed similar reformation of the healing amount than 3-D images compare with soft X-ray image. Among the four threshold values for 3-D images, 400-500 HU revealed similar reformation of the healing amount. Histopathologic examination confirmed the newly formed trabeculation correspond with imaging-based methologies. Conclusion: MPR images revealed higher accuracy of the imaging reformation of cone beam computed tomography and cone beam computed tomography is a clinically useful diagnostic tool for the assessment of bone defect healing.