The free cooling process in the inelastic hard sphere system is studied by analysing the data from large scale molecular dynamics simulations on a three dimensional system. The initial energy decay, the velocity distribution function, and the velocity correlation functions are calculated to be compared with theoretical predictions. The energy decay rate in the homogeneous cooling state is slightly but distinctively smaller than that expected from the independent collision assumption. The form of the one particle velocity distribution is found not to be stationary. These contradict to the predictions of the kinetic theory based on the Enskog-Boltzmann equation and suggest that the velocity correlation is already important in the early stage of homogeneous cooling state. The energy decay rate is analysed in terms of the velocity correlation.