To address the geohazard disaster risks and geothermal reservoir stability posed by the construction of artificial reservoirs in enhanced geothermal systems (EGS), the Yangbajing geothermal field in Xizang was selected as the research context. Focusing on the exploitation of naturally fractured geothermal reservoirs the problems were avoided related to artificial reservoir creation. A system of governing equations was established, and the accuracy of the mathematical model was verified to ensure the precision of numerical simulation. Physical parameters were defined based on the geological conditions of Yangbajing, and boundary conditions were configured according to the actual measurements from exploration wells ZK4001 and ZK4002. A three-dimensional model of a fractured geothermal reservoir was constructed. Numerical simulation methods were employed to investigate the dynamics of seepage and heat transfer dynamics within the fractured reservoir during geothermal extraction. The reservoir’s lifespan and heat extraction performance were predicted, a resource application scheme was proposed, and the impacts of well spacing, injection flow rate, and production pressure on efficiency were examined. The results indicate that the fracture network distribution is identified as the primary factor affecting geothermal extraction efficiency. The production lifespan of the simulated fractured reservoir is approximately 50 years, with a total extracted geothermal energy of 3.66×10¹⁰ MJ. In the multi-well production system, a clear distance attenuation effect is observed in the produced fluid temperature, with production wells located farther from the injection well maintaining higher output temperatures for a longer duration. Furthermore, the injection flow rate and production pressure are demonstrated to have significant impacts on the lifespan and output of the geothermal system. It is provided a theoretical basis for deep geothermal resources development and offers new insights for the efficient and sustainable utilization.