The mechanism of frictional energy dissipation holds notable importance in understanding the physical origins of nanofriction. Here, combining atomic force microscopy and Raman analysis, we confirm the important role of layer breathing modes in the layer-dependent frictional energy dissipation process of graphene layers. Then the LOZO′ mode is resonantly enhanced to elucidate the relationship between layer breathing modes and frictional energy dissipation from the perspective of phonon lifetime. The results indicate that phonon lifetime increases with the number of graphene layers, which is consistent with the increased stiffness and re-adjust configuration capability in thicker graphene stacks. Our findings provide compelling experimental evidence for the phononic energy dissipation in the friction of graphene layers, enhancing the understanding of dynamic dissipation processes at frictional interfaces.