Phonon transport and thermodynamic properties of nanostructured materials have been investigated and utilized to improve thermoelectric performance for various materials. In nanostructures, phonon transport is completely different from that in bulk materials and results in dramatic enhancement in the thermoelectric performance. This article reviews the impact of nanostructuring on the phonon transport and mainly focuses on phononic crystal nanostructures, in which the wave nature of phonons also plays an important role. We demonstrate that it is important to efficiently scatter thermal phonons, which distribute to wide range of frequencies, with different phonon scattering mechanisms in the spatial domain. We also demonstrate an enhancement of thermoelectric property of polysilicon thin films by phononic crystal patterning.