Abstract The evolution of the permeability of granite at high temperatures has a significant effect on geothermal exploitation. In this study, the fluid-solid coupling algorithm is improved based on the different intra-granular, inter-granular and crack seepage characteristics of granite, and the permeability characteristics of thermally treated granite specimens are simulated under different confining pressures. The results show that the permeability of granite non-linearly decreases with confining pressure in a concave type and its variation with temperature is similar to the experimental results. When T ≤ 300 °C, temperature has a slight effect on the variation of permeability. Because the temperature has a slight effect on the distribution characteristics of the flow rate and pore pressure, the flow rate mainly dependent on the inter-granular contact, which is parallel to the gradient of pore pressure. However, when T ≥ 450 °C, the number of thermally induced cracks increases and forms a coalesced channel; thus, the permeability increases with temperature. The temperature has a significant effect on the distribution characteristics of the flow rate and pore pressure. Confining pressure can decrease the permeability, whereas it has a slight effect on the distribution of flow rate and pore pressure in the specimen.