Porous materials are widely used in many heat transfer applications. Modeling porous materials at the microscopic level can accurately incorporate the detailed structure and substance parameters and thus provides valuable information for the complex heat transfer processes in such media. In this study, we use the generalized periodic boundary condition for pore-scale simulations of thermal flows in porous materials. A two-dimensional porous model consisting of circular solid domains is considered, and comprehensive simulations are performed to study the influences on macroscopic thermal conductivity from several microscopic system parameters, including the porosity, Reynolds number, and periodic unit aspect ratio and the thermal conductance at the solid–fluid interface. Our results show that, even at the same porosity and Reynolds number, the aspect ratio of the periodic unit and the interfacial thermal conductance can significantly affect the macroscopic thermal behaviors of porous materials. Qualitative analysis is also provided to relate the apparent thermal conductivity to the complex flow and temperature distributions in the microscopic porous structure. The method, findings and discussions presented in this paper could be useful for fundamental studies, material development, and engineering applications of porous thermal flow systems.