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A series of molecular dynamics (MD) simulations is conducted to investigate the dynamics of longitudinal optical (LO) phonon in Si nano-structure confined with oxide films. This work is motivated by heat issues in nanoscopic devices; it is considered that the LO phonons with low group velocity are accumulated in the nanoscopic device and the electric property deteriorates. We estimate the relaxation time of the LO phonon and investigate its dependency on the oxide thickness. The calculation results show that the LO phonon decays faster as the oxide thickness increases and turns into acoustic phonon. The result indicates that the presence of SiO2 films promotes the scattering of the phonon and this is effective to diminish the optical phonon.