This paper studies thermal transport in nanoporous silicon with a significant specific surface area. First, the equilibrium molecular dynamics approach was used to obtain the dependence of thermal conductivity on a specific surface area. Then, a modified phonon transport kinetic theory-based approach was developed to analyze thermal conductivity. Two models were used to evaluate the phonon mean free path in the porous materials. The first model assumes that the dependence of the mean free path only relies on the specific surface area, and the second one also considers the mean free path variation with the porosity. Both approaches approximate molecular dynamics data well for the smaller porosity values. However, the first model fails for highly porous matrixes, while the second one matches well with molecular dynamics simulations across all considered ranges of the porosities. This work illustrates that the phonon mean free path dependence with the porosity/volume fraction of composite materials is essential for describing thermal transport in systems with significant surface-to-volume ratio.