Controlling the thermal conductivity of thermoelectric materials continues to be a goal for energy conversion applications. The Phonon Boltzmann Transport Equation is solved by using the Discrete Ordinates Method to numerically study the phonon thermal conductivity of nanostructured silicon thin film with pores in this study. The effects of the film thickness, film porosity, and porous structure are concerned. The numerical results show that the nano-pores are able to reduce the thermal conductivity of the silicon thin film sharply by the phonon boundary scattering, and the scattering boundary area has significant effect on the thermal conductivity. The method of local angle distribution between heat fluxes is introduced for the first time to optimize the pore placement for reducing the thermal conductivity. V