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It is well known that the complicated channeling of fluid flow and heat transfer is strongly related with the intricate natural fracture system. However, it is still challenging to set up the fracture network model which is strong heterogeneous. Compared with other methods (e.g. equivalent continuum model (ECM), discrete fracture model (DFM), and ECM-DFM), the fracture flow module in the COMSOL Multiphysics simulator is powerful in definition of fractures as the inner flow boundary existing in the porous media. Thus it is selected to simulate the fluid flow and heat transfer in the geothermal-developed fractured granite of Sanguliu area located at Liaodong Peninsula, Eastern China. The natural faults/fractures based on field investigation combined with the discrete fracture network (DFN) generated by the MATLAB are used to represent the two-dimensional geological model. Numerical results show that early thermal breakthrough occurs at the production well caused by quick flow of cold water along the highly connected fractures. Suitable hydraulic fracturing treatments with proper injection rates, locations, etc. can efficiently hinder the thermal breakthrough time in the natural fracture system. Large well spacing helps the long-term operation of geothermal production, but it is highly dependent on the geometrical morphology of the fracture network. The enhancement of reservoir properties at the near-well regions can also increase the geothermal production efficiency. The results in this study can provide references to achieve a sustainable geothermal exploitation in fractured granitic geothermal reservoirs or hot dry rocks at depth.