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The phonon dispersion relation in 〈100〉 Si nanowire (SiNW) is calculated by employing a realistic atomistic model surrounded by thin SiO2 layer. We performed molecular dynamics simulations to calculate the dynamical structure factor by the space-time Fourier transform of atomic trajectories, and extracted the phonon dispersion relations. In the SiNWs, low energy phonon branches spread into broad spectra due to the presence of the SiO2 film, which is considered as the origin of the thermal conductivity degradation. A softening of the transverse optical mode also appears due to the lattice strain induced by the outer oxide film. This work suggests that the presence of amorphous oxide layer is crucial factor to characterize phonon vibration properties in practical SiNWs.