Molecule-substrate interaction channels of metal-phthalocyanines (MPcs, including NiPc, CuPc, ZnPc, FePc, and CoPc) on graphene on Ni(111) were investigated by employing high-resolution electron energy loss spectroscopy (HREELS). Except the expected IR-active modes, some Raman-active modes were also observed in all of MPcs, which are considered in this study. From the origination of the Raman-active features, it was deduced that MPcs are coupled with the substrate mainly through their central metal atom. The Raman-active modes appear as symmetric peaks in the HREELS in the case of MPcs with Ni, Cu, and Zn, whereas they are asymmetric and appear as a Fano line shape in the case of MPcs with Fe and Co. This spectroscopic difference indicates that the molecule-substrate coupling is completely different in the two cases mentioned above. The molecule-substrate interaction strength is considerably weak and comparable with the π-π interaction between molecules in the case of MPcs with Ni, Cu, and Zn, whereas it is much stronger in the case of MPcs with Fe and Co. From the HREELS observations, it can be suggested that the whole molecule can be effectively decoupled from the underneath Ni(111) by inserting a single layer of graphene between them in the case of MPcs with Ni, Cu, and Zn, whereas only benzene rings can be completely decoupled in the case of MPcs with Fe and Co.