The Phonon Boltzmann Transport Equation (BTE) is solved by using the Discrete Ordinates Method to numerically study the phonon thermal conductivity in nanoporous silicon thin film and nanocomposites. The frequency-dependent phonon transport is considered to solve the phonon BTE. We study the effect of pore geometry on phonon energy transport in silicon thin film by fixing the porosity and interface area, respectively. The thermal conductivity in three-dimensional thin film are numerically computed by considering the size effect and we show the difference by comparing the results with those of two-dimensional thin film. The thermal conductance in the third direction is taken into account in the three-dimensional silicon thin film, which is more accurate than the two-dimensional thin film model. The phonon BTE model is also employed to study the thermal conductivity of three-dimensional nanocomposites (silicon nanoparticles embedded in Germanium host matrix). The effects of the nanocomposite size, silicon percentage, and the interface area on the thermal conductivity are discussed.