Nanostructured materials exhibit low thermal conductivity because of the additional scattering due to phonon-boundary interactions. As these interactions are highly sensitive to the mean free path (MFP) of a given phonon mode, MFP distributions in nanostructures can be dramatically distorted relative to bulk. Here we calculate the MFP distribution in periodic nanoporous Si for different temperatures, using the recently developed MFP-dependent Boltzmann Transport Equation. After analyzing the relative contribution of each phonon branch to thermal transport in nanoporous Si, we find that at room temperature optical phonons contribute 18 % to heat transport, compared to 5% in bulk Si. Interestingly, we observe a steady thermal conductivity in the nanoporous materials over a temperature range 200 K < T < 300 K, which we attribute to the ballistic transport of acoustic phonons with long intrinsic MFP. These results, which are also consistent with a recent experimental study, shed light on the origin of the reduction of thermal conductivity in nanostructured materials, and could contribute to multiscale heat transport engineering, in which the bulk material and geometry are optimized concurrently.