C60 molecules adsorbed on graphene/Ru(0001) substrate were investigated by scanning tunneling microscopy (STM) at 5 K. On high quality substrates, C60 molecules adopt a commensurate growth mode, leading to formation of a supramolecular structure with perfect periodicity and few defects. On under-annealed substrates with imperfections and domains, the molecules form the same closely packed hexagonal structures in spite of underlying corrugations, disorders or steps, indicating a weak molecule-substrate interaction—a conclusion that is also supported by DFT calculations. This system may be beneficial to the fabrication of carbon based devices and of other types of organic functional overlayers.