The study of the seepage and heat transfer law of three-dimensional rough fractures is of great significance in improving the heat extraction efficiency of underground thermal reservoirs. However, the phase transition effects of fluids during the thermal exploitation process profoundly influence the intrinsic mechanisms of fracture seepage and heat transfer. Based on the FLUENT 2020 software, single-phase and multiphase heat–flow coupling models were established, and the alterations stemming from the phase transition in seepage and heat transfer mechanisms were dissected. The results indicate that, without considering phase transition, the geometric morphology of the fractures controlled the distribution of local heat transfer coefficients, the magnitude of which was influenced by different boundary conditions. Moreover, based on the Forchheimer formula, it was found that the heat transfer process affects nonlinear seepage behavior significantly. After considering the phase transition, the fluid exhibited characteristics similar to shear-diluted fluids and, under the same pressure gradient, the increment of flow rate was higher than the increment in the linearly increasing scenario. In the heat transfer process, the gas volume percentage played a dominant role, causing the local heat transfer coefficient to decrease with the increase in gas content. Therefore, considering fluid phase transition can more accurately reveal seepage characteristics and the evolution law.