Graphene as the thinnest material has an extremely large specific surface area, and thus the physical properties of graphene based devices should be sensitively dependent on the contacted metals. Moreover, the interfacial interaction between graphene and metals is complicated and it is difficult to probe. In this paper, epitaxial graphene is prepared by thermal decomposition of 6H-SiC(0001), and then Ag is deposited on it. It is found that the morphology and distribution of Ag particles on graphene domains are independent of the graphene thickness. The Ag particles induce the surface enhanced Raman scattering (SERS) effect and the doping effect in epitaxial graphene. The enhancement factor of SERS as well as the splitting of the G band and the shift of the 2D band decreases with increasing graphene thickness, which can be ascribed to the weakened interaction between Ag and EG. This is confirmed by the charge transfer between the Ag atom and epitaxial graphene on 6H-SiC predicted by first-principles calculations. The results are helpful to the design and development of graphene-based composites and devices.