In order to estimate long-term hydraulic properties of rocks, we carried out the comparison between a permeable fracture and a low-permeable fracture filled by calcite, and evaluated three-dimensional structure of both fractures by means of X-ray computed tomography. As a result, the low-permeable fracture function as permeable fracture because the joint is connected to each other as channel. Furthermore, the permeability of fracture filled by calcite is the potentially same permeability of permeable fracture since the calcite dissolve in the longer term.