The inclusions in a high-temperature resistant matrix can significantly influence the radiative heat transfer of composite materials at elevated temperatures; therefore, the microstructure design of composites for thermal protection during atmospheric re-entry require a more accurate prediction of thermal insulation performance. In this paper, the Rosseland approximation was used to investigate the radiative heat transfer within thermal protection materials, e.g., porous carbon-based material and ultra-high-temperature ceramics (e.g., ZrB2-SiC), and the discrete dipole scattering method was used to evaluate the extinction efficiency across the inclusions with different types of microstructures. The effect of inclusion parameters, such as inclusion size, shape coefficient, volume fraction, orientation, and size distribution, on the radiative and effective thermal conductivity (ETC) at various temperatures was analyzed in detail. Test results obtained from the existing literature were used to validate the ETC of porous ceramics predicted by the proposed model. The results indicated that the microstructures in thermal protection materials play a fundamental role in improving the heat-shielding properties. The present study deepens the understanding of the relationship between microstructures and thermal radiation properties and provides theoretical design guidelines for thermal protection materials with improved thermal insulation properties.