We propose a novel technique of molecular dynamics simulation to evaluate the relaxation time of phonons in solids for investigation of solid heat conductivity. The basic idea is to observe relaxation behavior of the power spectrum of atomic velocities after energetically stimulating modes in a specific frequency region. The transient entropy S(t) is defined with the power spectrum based on non-equilibrium statistical mechanics to quantitatively evaluate the relaxation speed. In this paper, two example systems are shown; Lennard-Jones model crystal and silicon crystal. For both systems, we found that the observed S(t) is well fitted to a single exponential function, from which we can obtain a frequency-dependent relaxation time.