Atomistic mechanisms of frictional energy dissipation have attracted significant attention. However, the dynamics of phonon excitation and dissipation remain elusive for many friction processes. Through systematic fast Fourier transform (FFT) analyses of the frictional signals as a silicon tip sliding over a graphite surface at different angles and velocities, we experimentally demonstrate that friction mainly excites non-equilibrium phonons at the washboard frequency and its harmonics. Using molecular dynamics (MD) simulations, we further disclose the phononic origin of structural lubrication, i.e., the drastic reduction of friction force as the contact angle between two commensurate surfaces changes. In commensurate contacting states, friction excites a large amount of phonons at the washboard frequency and many orders of its harmonics that perfectly match each other in the sliding tip and substrate, while for incommensurate cases, only limited phonons are generated at mismatched washboard frequencies and few low order harmonics in the tip and substrate.