We have calculated the mean free path (MFP) of phonons associated with boundary scattering in polycrystalline nanostructures. A numerical transmission model, based on the kinetic theory and the Landauer's formula, was developed to obtain the phonon MFP. The MFP in a simple cubic polycrystalline nanostructure was calculated and compared with that of the previously-formulated analytical model derived from Matthiesen's rule with combining scatterings effect of super lattice and nanowire. The results show that the MFP of our calculations is around 0.6〜0.9 times that of the model. It is due to the limitation of the rule on combining two anisotropic scatterings. We have also revealed how the geometric complexity and grain-size distribution influence the MFP by performing simulations for nanostructures generated with Voronoi diagram. It is shown that the MFP in complex nanostructures with a realistic grain-size distribution is at most 20% longer than that in a mono grain-size structure with the same average grain size.