We demonstrate that highly surface-sensitive supersonic rare-gas (He, Ar, and Xe) atom scattering, in both the quantum and classical regimes, can probe and quantify the interlayer interactions between graphene monolayers and metal substrates in terms of the Debye temperature corresponding to the surface normal vibration, and the surface effective mass. As models of the strongly and weakly interacting graphene, we investigated two systems, graphene on Ru(0001) and Pt (111), respectively. The experimental data for Ar and Xe are compared with the results from theoretical simulations based on the classical smooth surface model. For gr/Pt(111) we find that the scattering pattern of the rare-gas beam, including the Debye-Waller attenuation of the He beam, are quite similar to that from highly oriented pyrolytic graphite (HOPG); this suggests that the graphene-Pt (111) interaction is much like a van der Waals interaction. On the contrary, for the gr/Ru(0001) system, we find a smaller Debye-Waller attenuation and a larger surface effective mass, indicating that graphene on Ru(0001) is tightly bonded to the substrate. Furthermore, asymmetrical spectral shapes in the Ar and Xe scattering spectra from gr/Ru(0001) are interpreted as a result of the lateral distribution of the interlayer interaction corresponding to the moiré pattern. It is found that the "valley" region of the moiré pattern has high effective mass reflecting stronger bonding to the substrate, contributing to the high reflectivity of the He beam reported for this system. On the other hand, the effective mass of the "hill" region is found to be similar to that of HOPG, indicating that this region is well decoupled from the substrate. These results demonstrate a unique capability of atom scattering to probe and evaluate the molecule-substrate interaction and its spatial distributions.