As nanostructured devices become prevalent, interfaces often play an important role in thermal transport phenomena. However, interfacial thermal transport remains poorly understood due to complex physics across a wide range of length scales from atomistic to microscale. Past studies on interfacial thermal resistance have focused on interface-phonon scattering at the atomistic scale but overlooked the complex interplay of phonon-interface and phonon-phonon scattering at microscale. Here, we use the Peierls-Boltzmann transport equation to show that the resistance from the phonon-phonon scattering of non-equilibrium phonons near a Si–Ge interface is much larger than that directly caused by the interface scattering. We report that non-equilibrium in phonon distribution leads to significant entropy generation and thermal resistance upon three-phonon scattering by the Boltzmann's H-theorem. The physical origin of non-equilibrium phonons in Ge is explained with the mismatches of phonon dispersion, density-of-states, and group velocity, which serve as general guidance for estimating the non-equilibrium effect on interfacial thermal resistance. Our study bridges a gap between atomistic scale and less studied microscale phenomena, providing comprehensive understanding of overall interfacial thermal transport and the significant role of phonon-phonon scattering.