Abstract: To clarify the differences in seepage and heat transfer between water and supercritical carbon dioxide (ScCO₂) in deep carbonate geothermal reservoirs and to identify the evolution of the seepage field in complex fracture networks under the combined effects of temperature, confining pressure, fluid properties, and fracture structure, carbonate rocks from the Honghuayuan, Lunshan, and Guanyintai formations in Jurong, Jiangsu Province, were prepared as 100 mm × 100 mm × 100 mm cubic specimens. Comparative experiments were conducted using a high-temperature and high-pressure true-triaxial integrated apparatus for fracturing, seepage, and heat transfer. In the confining-pressure tests, the temperature was maintained at 100 ℃, and four triaxial stress states of 5/10/15, 8/14/20, 10/16/22, and 14/20/26 MPa were applied. In the temperature tests, the triaxial stress state was fixed at 5/10/15 MPa, and five temperature levels of 60, 80, 100, 120, and 140 ℃ were adopted. Water was injected at a constant flow rate of 15 mL/min, whereas ScCO₂ was injected at a constant pressure of 7.4–7.7 MPa. The equivalent hydraulic aperture, apparent convective heat-transfer coefficient, and heat-transport efficiency were calculated from the measured flow rate, pressure difference, and inlet and outlet temperatures. Acoustic-emission localization, three-dimensional computed-tomography reconstruction, and permeability-tensor analysis were combined to determine the effects of fracture number, orientation, and connectivity on the seepage field. Increasing confining pressure reduced the equivalent hydraulic aperture, flow velocity, apparent convective heat-transfer coefficient, and heat-transport efficiency of both fluids, with the rate of reduction gradually decreasing at higher stress levels. The equivalent hydraulic aperture of ScCO₂ was more sensitive to changes in confining pressure. For specimen HHY-8, the hydraulic aperture of water decreased by 1.4%, 0.3%, and 0.1% during successive loading stages, whereas that of ScCO₂ decreased by 10.5%, 3.5%, and 1.5%, respectively. As the temperature increased from 60 ℃ to 140 ℃, mineral thermal expansion continuously reduced the equivalent hydraulic aperture, while the increased temperature difference between the rock and the working fluid generally enhanced the apparent convective heat-transfer coefficient and heat-transport efficiency. The temperature-induced reduction in hydraulic aperture increased with dolomite content. ScCO₂ exhibited a higher apparent convective heat-transfer capacity than water under most temperature and pressure conditions. At 140 ℃, however, decreases in the density and isobaric specific heat capacity of ScCO₂ caused the heat-transport efficiency of water to become generally higher than that of ScCO₂. Permeability-tensor calculations showed that, for specimen LS-1, the permeability coefficient of water decreased from 12.71 m/d at 60 ℃ to 4.88 m/d at 140 ℃, whereas that of ScCO₂ decreased from 8.39 m/d to 6.22 m/d. Fracture number exerted a stronger control on flow capacity at low confining pressure, whereas fracture-orientation combinations, connectivity, and hydraulic communication with the borehole became more important at high confining pressure. Temperature had a weaker effect on the principal seepage direction and the overall seepage field than confining pressure. Seepage and heat transfer in fractured carbonate geothermal reservoirs are jointly controlled by mechanical fracture closure, mineral thermal expansion, and the thermophysical properties of the working fluid. ScCO₂ provides higher apparent heat-transfer performance at low and moderate temperatures, but its heat-transport advantage weakens with increasing temperature. Working-fluid selection should therefore comprehensively account for reservoir temperature, stress state, mineral composition, and fracture-network structure.