Although the friction characteristics under different contact conditions have been extensively studied, the mechanism of phonon transport at the structural lubrication interface is not extremely clear. In this paper, we firstly promulgate that there is a 90°-symmetry of friction force depending on rotation angle at Si/Si interface, which is independent of normal load and temperature. It is further found that the interfacial temperature difference under incommensurate contacts is much larger than that in commensurate cases, which can be attributed to the larger interfacial thermal resistance (ITR). The lower ITR brings greater energy dissipation in commensurate sliding, and the reason for that is more effective energy dissipation channels between the friction surfaces, making it easier for the excited phonons at the washboard frequency and its harmonics to transfer through the interface. Nevertheless, the vibrational frequencies of the interfacial atoms between the tip and substrate during the friction process do not match in incommensurate cases, and there is no effective energy transfer channel, thus presenting the higher ITR and lower friction. Eventually, the number of excited phonons on contact surfaces reveals the amount of frictional energy dissipation in different contact states.