It is necessary to evaluate the change of fracture roughness surfaces within a rock when estimating the hydro-mechanical properties of rock masses in a long-term. The fracture contact-area condition and the fracture aperture under the coupled conditions are needed. The evaluation of the structure and the flow evolution of rock fracture under confining pressure conditions is insufficient. Therefore, a triaxial cell with heating capabilities that can be installed on the work table of the microfocus X-ray CT (μX-ray CT) is developed to grasp the fracture change in a long-term under various confining conditions. A single fracture of a rock is conducted several permeability tests and is also profiled through μX-ray CT under normal temperature and confining conditions. The contact points have been evaluated by the CT observation, and the contact ratios of this fracture, the aperture distribution are estimated. In addition, The flow simulations are conducted from the observed CT data, and the shape of the flow variations in a long-term are obtained.