Objective：To compare the results of bone regeneration condition in mouse calvarial defects measured by Mimics or Micro-CT scanner’s built-in software and to evaluate the differences of the two methods. Methods：Defect of 4 mm in diameter was prepared on the right cranium of mice，and in vivo Micro-CT scan was performed immediately after surgery，6 weeks and 12 weeks postopera－tively. Then new bone volume and bone healing rate within the defect were measured after reconstructing 3D images by Micro-CT scanner’s built-in software. The new bone volume and bone healing rate within the defect were quantitatively analyzed using Mimics software. The 2D data of Micro-CT were imported into Mimics software and 3D images were reconstructed by it as well. Results：The bone regeneration volume and bone healing rate at 12 weeks postoperatively were significantly higher than those at 6 weeks postoper－atively，no matter measured by Micro-CT scanner’s built-in software or Mimics software（P<0.05）. In addition，there was no signifi－cant difference in the new bone volume and bone healing rate between the results of Mimics software and the results of Micro-CT scanner’s built-in software at 6 weeks and 12 weeks postoperatively（P<0.05）. Conclusion：Similar results of new bone regeneration within the calvarial defect are obtained by the two softwares at 6 weeks and 12 weeks postoperatively . However，mimics software is simpler to operate than Micro-CT scanner’s built-in software.