The phonon dispersion relation in <100> Si nanowire (SiNW) is calculated by employing a realistic atomistic model surrounded by thin SiO 2 layers. We performed molecular dynamics simulation to calculate the dynamical structure factor by the space-time Fourier transform of atomic trajectories, and extracted the phonon dispersion relations. Although the bulk dispersion relations are maintained in the SiNWs on the whole, acoustic phonon branches are diffused beyond recognition, which is considered as the origin of the thermal conductivity degradation in SiNWs. A red shift of the transverse optical mode also appears probably due to the lattice strain induced by the outer oxide film. These results provide a foothold to estimate the electron-phonon scattering rates and the heat transport processes in realistic SiNWs.