Si-based nanoporous semiconductors have attracted great attentions recently due to their prominent properties and great potentials in thermoelectric applications. We have systematically investigated the transversal thermal transport in crystalline Si with nanocylindrical pore arrays using nonequilibrium and equilibrium molecular dynamics simulations together with lattice dynamics calculations. It is found that nanoporous Si with anisotropic pore pitches shows a remarkable tunable anisotropy in phonon transport, mainly due to the different reductions in phonon relaxation times by the channel confinement. Meanwhile, the significant decrease in thermal conductivity is caused by both the zone folding and the suppression of relaxation times. The analysis on the temperature distributions and profiles shows that the major thermal resistance is from the channel region while ballistic phonon transport is important for the other regions. Additional scattering caused by the junctions leads to an effective thermal conductivity considerably lower than that predicted by only considering diffusive boundary scattering and also enhances the anisotropy. This anomaly is attributed to the phonon dispersion mismatch and can be quantitatively modeled by a scalar model of the elastic waves, implying the importance of phonon wave behavior at nanoscale. By considering all the scattering mechanisms, a structure-based two-part model has been developed to predict the thermal conductivity in nanoporous structures, which shows good agreements with molecular dynamics results and can be readily extrapolated to meso/macro systems. The anisotropy and junction effects in nanoporous structures provide a new strategy in tailoring the thermal properties of materials for targeted applications. (C) 2014 Elsevier Ltd. All rights reserved.