In deep geological disposal system designs, it is important to minimize the installation area for cost effectiveness while satisfying the thermal requirements of the systems. An effective method to reduce the installation area for the systems is to employ an enhanced buffer material, as this can decrease the spacing between the disposal tunnels and deposition holes. Therefore, this study aims to evaluate the effect of an enhanced buffer material on the thermal behavior of the systems and their spacing. First, the discrete element method (DEM) was adopted to validate the thermal conductivity of the enhanced buffer material used, which was a mixture of bentonite and graphite. Then, a 3D finite element method (FEM) was conducted to analyze the proper disposal tunnel and hole spacing considering three cases with thermal conductivities values of the buffer as 0.8 W/(m K), 1.0 W/(m K), and 1.2 W/(m K). The results showed that the disposal tunnel and hole spacing could be reduced to 30 m and 6 m, respectively, when the temperature of the buffer surface facing the canister was 100 °C with a thermal conductivity value of approximately 1.2 W/(m K) or if more than 3% of graphite is added.