This study analyzes the phonon radiative transfer in two-dimensional porous silicon nanostructures with a phonon transport model based on the Boltzmann transportation equation. We focus on the inter-scattering between pores. The numerical results show that when the aspect ratio is less than 1.22, the scale factor dominates the thermal conductivity, and the thermal conductivity of nanostructures with in-line arrangement pores is determined by the dependent phonon scattering effect. In nanostructures with staggered arrangement pores, the phonons are prevented from transporting through the material. In general, the results show that the larger the pore size, the lower the thermal conductivity of the nanostructure. The results presented in this study provide a useful reference for the development of high-efficiency thermoelectric structures. (C) 2008 Elsevier Ltd. All rights reserved.