Whether the shear displacement can exert a significant control on the fault hydraulic conductivity of rocks or not is common major concerns in both engineering fields and earth science fields. To clarify the relation between hydraulic conductivity and inner structures in rocks, we have measured three principal strains and hydraulic conductivity in the intermediate principal stress direction during deformation as a function of three principal stresses. The specimens were deformed under the true triaxial compression stress state where the intermediate principal stress is not equal to either the minimum or the maximum principal stress. In brittle faulting regime, the hydraulic conductivity decrease with increasing the axial strain until the onset of dilatancy, then increase significantly with increment of the axial strain. In the specimens under the effective confining pressure lower than 10 MPa, the final hydraulic conductivity value is larger than the initial value. On the other hand, in both brittle-ductile transition and fully ductile regimes the hydraulic conductivity after the onset of dilatancy increases slightly. Deformation experienced or failure induced specimens show a final value lower than the initial value before the deformation. We used X-Ray CT with high resolution of only 10 micron to visualize the fracture pattern in the stressed specimen. Using 2D images obtained by X-Ray CT, we can get easily more detail information about inner structure change caused by the difference with three principal stresses.