To avoid any shortcuts that may “short-circuit” the fluid flow between the injection and production wells in an enhanced geothermal system (EGS), we explore the idea of autonomous in-situ tunning of fracture hydraulic conductivity (FCTT) and its potential benefits. The new technique is expected to provide variable fracture hydraulic conductivity depending on the surrounding temperature. Through FCTT, we can effectively manage the fluid flow in the reservoir and promote a uniform thermal gradient along the flow paths. A numerical finite element model is established to assess the impact of tunning magnitude and fracture network geometries on the production efficiency of EGSs. Results show that utilizing this technique could prevent an early appearance of fluid flow shortcut between injector and producer in an EGS. After 50 years of production, the output thermal power with the technique could be increased by 67.51%. Furthermore, we found that fracture density and fracture network connectivity in the reservoir could affect performance improvement reached by FCTT in production. We also present a field case with a realistic fracture network. After 50 years of production, applying this technique increases heat extraction by 101.78% in fracture networks that are expected in EGS. Since other flow-control systems in geothermal production are mainly focused on the wellbore and near-wellbore areas, this technique can provide a more effective enhancement in heat extraction by controlling flow deep inside the reservoir.