The fate of superconductivity of a nanoscale superconducting film/island relies on the environment; for example, the proximity effect from the substrate plays a crucial role when the film thicknesses is much less than the coherent length. Here, we demonstrate that atomic-scale tuning of the proximity effects can be achieved by one atomically thin graphene layer inserted between the nanoscale Pb islands and the supporting Pt(111) substrate. By using scanning tunneling microscopy and spectroscopy, we show that the coupling between the electron in a normal metal and the Cooper pair in an adjacent superconductor is dampened by 1 order of magnitude via transmission through a single-atom-thick graphene. More interestingly, the superconductivity of the Pb islands is greatly affected by the moire patterns of graphene, showing the intriguing influence of the graphene-substrate coupling on the superconducting properties of the overlayer.