Underground space creation and energy extraction, which induce unloading on rock fractures, commonly occur in various rock engineering projects, and rock engineering projects are subjected to high temperatures with increasing depth. Fluid flow behavior of rock fractures is a critical issue in many subsurface rock engineering projects. Previous studies have extensively considered permeability evolution in rock fractures under loading phase, whereas changes in fracture permeability under unloading phase have not been fully understood. To examine the unloading-induced changes in fracture permeability under different temperatures, we performed water flow-through tests on fractured rock samples subjected to decreasing confining pressures and different temperatures. The experimental results show that the permeability of fracture increases with unloading of confining pressure but decreases with loading-unloading cycles. Temperature may affect fracture permeability when it is higher than a certain threshold. An empirical model of fracture hydraulic aperture including two material parameters of initial normal stiffness and maximum normal closure can well describe the permeability changes in rough rock fracture subjected to loading-unloading cycles and heating. A coupled thermo-mechanical model considering asperity damage is finally used to understand the influences of stress paths and temperatures on fracture permeability.