In order to elucidate the mechanism of low thermal conductivity caused by nanostructures and nano-stractural clearances, we calculated thermal conductivity, a phonon dispersion relationship. and density of states in model thin film depending on nanostructures and nano-structual clearances by the classical molecular dynamics simulation (MD).We can observe some change of the group velocity of partial phonon in the phonon dispersion relations of the longitudinal wave as well as the reduction of thermal conductivity when the nano structural clearance was relatively small.