The phonon dissipation is investigated through molecular dynamics (MD) simulation modeling graphene flake sliding on supported graphene in this paper. With the help of the advantage of MD, we explore the phonon mode variation of the substrate induced by the behavior of friction in terms of phonon densities of states. Moreover, phonon dissipation modes connected with the relative sliding velocity and the temperature of system are established respectively. The simulation results demonstrate phonon dissipation is represented as special phonon frequencies while those are closely related to the sliding velocities but would not shift as the change of temperatures. For an explanation of the special frequencies, we further simplify the model by directly adding the velocity to the atoms of the flake in the MD model, although it is impractical. It is found that a special frequency of phonon dissipation is generally in agreement with the sliding frequency at low temperature eliminating the interference of temperature in a range of velocities from 50m/s to 250m/s, namely, the velocity is directly related to the modes of phonon dissipation and friction, which is consistent with the previously reported result[1] that the velocity is an influence factor for friction both in experimental and theoretical researches. Therefore, the relationship makes possible the active control of friction. It is the first step toward using this method to reveal the fundamental questions in the study of atomic-scale friction.