Due to their intrinsically incommensurate interfaces, two-dimensional van der Waals heterostructures are promising candidates for achieving stable structural superlubricity. However, substantial differences in interlayer friction are still observed among different heterostructures. In this study, nonequilibrium molecular dynamics simulations were employed to investigate, at the atomic scale, how phonon-mediated dissipation governs frictional behavior. The results show that in the MoS2/PdSe2 heterostructure, stronger interlayer interactions and larger substrate potential corrugation make the friction process more strongly dominated by the substrate potential, resulting in a higher friction force and friction coefficient. In contrast, the graphene/MoS2 and graphene/PdSe2 heterostructures exhibit smoother potential energy surfaces, and their frictional behavior is governed mainly by the resonant vibration of the cantilever-probe system. Increasing the normal load enhances friction by increasing the interfacial potential corrugation and the associated mechanical work, which is dissipated through amplified excitation of substrate phonons at the washboard frequency. Among the three systems, MoS2/PdSe2 exhibits the most pronounced increase in the phonon population at this frequency, corresponding to a higher friction coefficient and a more pronounced linear load dependence. Increasing the sliding velocity enhances energy dissipation by increasing both the frequency and the population of low-frequency phonons. When a harmonic of the washboard frequency approaches the natural frequency of the cantilever-probe system, resonance is triggered, leading to a peak in friction force. This work clarifies the phonon-mediated dissipation mechanisms in different two-dimensional van der Waals heterostructures and provides new insights into the understanding and regulation of interfacial friction.