Summary Hydraulic‐fracturing treatments have become an essential technology for the development of deep hot dry rocks (HDRs). The deep rock formation often contains natural fractures (NFs) at micro and macroscales. In the presence of the NF, the hydraulic‐fracturing process may form a complex fracture network caused by the interaction between hydraulic fractures and NF. In this study, analysis of carbon dioxide (CO2)‐based enhanced geothermal system (EGS) and water‐based EGS in complex fracture network was performed based on the thermo‐hydro‐mechanical (THM) coupling method, with various rock constitutive models. The complexity of the fracture geometry influences the fluid flow path and heat transfer efficiency of the thermal reservoir. Compared with CO2‐based EGS, water‐based EGS had an earlier thermal breakthrough with a rapid decline in production temperature. CO2 can easily gain heat rising its temperature thus reducing the effect of a premature thermal breakthrough. Both CO2‐based EGS and water‐based EGS are affected by in‐situ stress; the increase in stress ratio improved the fracture permeability but resulted in an early cold thermal breakthrough. When the same injection rate is applied to water‐based EGS and CO2‐based EGS, water‐based EGS displayed higher injection pressure buildup. Water‐based EGS had higher reservoir deformation area than CO2‐based EGS, and thermoelastic constitutive model for water‐based EGS showed larger deformed area ratio than thermo‐poroelastic rock model. Furthermore, higher values of rock modulus accelerated the reservoir deformation for water‐based EGS. This study established a novel discussion investigating the performance of CO2‐based EGS and water‐based EGS in a complex fractured reservoir. The findings from this study will help in deepening the understanding of the mechanisms involved when using CO2 or water as a working fluid in EGS. This paper showed that water‐ based enhanced geothermal system (EGS) had significant injection pressure buildup and higher reservoir deformation due to the flow behavior and properties of water in the thermal reservoir. CO2‐based EGS had a delayed thermal breakthrough than water‐based EGS, CO2 can easily gain heat thus reducing the effect of a premature thermal breakthrough. The thermoelastic or thermo‐poroelastic constitutive models influence the level of simulated results and they should be applied in accordance to the rock mineral constituents.