Osseointegration has been used as an index for prediction of long-term success of implant. Osseointegration has been routinely evaluated by measuring bone contact ratio on histology based on two-dimensional (2D) sections or images. However, these both methodologies have been less informative analysis of results and have several disadvantages. The aim of this study is to introduce new methodology for evaluation of a degree of osseointegration between bone and implant based on micro computed tomography (${mu}$-CT) images. Specimen was scanned at a voxel resolution of $35;{mu}m$ by ${mu}$-CT. Three-dimensional (3D) models of bone and implant were reconstructed respectively. Bone contact area (BCA) and bone contact area ratio (BCAR) were measured and calculated. Here, osseointegrated BCA between bone and implant surfaces was determined by computing areas of all bone regions existed within $35;{mu}m$ distance from implant surface. Osseointegration of flapless implant surgery was evaluated by new methodology, compared with that of flap implant surgery. BCA and BCAR in flapless implant surgery was significantly bigger than that in flap implant surgery (p<0.05), suggesting that flapless implant surgery was more effective than flap implant surgery consistent with previous studies. In the conclusion, new methodology for evaluation osseointegration between bone and implant based on ${mu}$-CT images was likely to be reliable, useful and more informative analysis of results.