As a relatively new type of functional material, porous graphite foam exhibits unique thermophysical properties. It possesses the advantages of low density, high specific surface area, and high bulk thermal conductivity and could be used as the core component of compact, lightweight, and efficient heat exchangers. Effective thermal conductivity serves one of the key thermophysical properties of foam-based heat exchangers. The complex three-dimensional topology and interstitial fluids significantly affect the heat conduction in the porous structure, reflecting a topologically based effective thermal conductivity. This paper presents a novel geometric model for representing the microstructure of graphite foams with simplifications and modifications made on the realistic pore structure, where the complex surfaces and tortuous ligaments were converted into a simplified geometry with cylindrical ligaments connected between cuboid nodes. The multiple-layer method was used to divide the proposed geometry into solvable areas, and the series–parallel relation was used to derive the analytical model for the effective thermal conductivity. To explore heat conduction mechanisms at the pore scale, direct numerical simulation was also conducted on the realistic geometric model. Achieving good agreement with experimental data, the simplified geometric model was validated. The numerically simulated conductivity followed the simplified model prediction that the two geometries are equivalent from thermal aspect. It validates further that the simplified model is capable of reflecting the internal microstructure of graphite foam, which would benefit the understandings of the thermophysical mechanisms of pore-scaled heat conduction and microstructures of graphite foam.