This study investigates the permeability behaviors of fractured granite, which is crucial for a multitude of subsurface applications such as nuclear waste disposal. The research integrates short-term and long-term observations conducted under diverse experimental conditions. Furthermore, by employing a combination of X-ray CT equipment and traditional flow-through tests, real-time monitoring of rock samples under varying experimental conditions has been achieved. In the short-term, controlled laboratory tests were conducted, involving fractured granite specimens subjected to controlled confining pressure cycles ranging from 0 to 3 MPa, and exposed to temperatures of 25 and 60 °C. Simultaneously, X-ray CT tests were employed during each flow-through test to capture real-time changes in the sample’s internal structure. The findings reveal a reversible behavior with a strong dependence on both confining pressure and temperature. In the long-term test, the study conducted continuous permeability tests over several months, during which effluent element concentrations were consistently monitored, and X-ray CT scans were performed at various stages of the experiments. The results exhibited a continuous decrease trend with some irregular variations, which were attributed to changes caused by pressure dissolution and precipitation and solution at free surfaces. These complex phenomena were further investigated through numerical simulations.