To investigate the cooling mechanism and the local structural changes of excimer laser-annealed silicon (Si), molecular dynamics (MD) simulations were performed. Heat flow of molten Si showed a strong dependency of the local region during a natural cooling. An amorphous-to-liquid transition near an interface in the temperature range of 1600 K ∼ 1800 K was expected with the results of the local diffusion coefficients calculated by integrating the velocity autocorrelation functions. It was confirmed that the structure of the interface region affected the cooling rate of the overall system. The structural properties at the various local regions after a cooling were assessed in terms of the configurational properties including the coordination and bond-angle distributions. A spontaneous nucleation of Si near a interface was observed during a natural cooling.