[en] In this paper, the study of using masks to directly generate large area, highly ordered and periodical nanostructure has been exhibited. Periodic Au nano-discs(NDs) arrays have been fabricated on top of graphene by using holey Si₃N₄ mask which is directly fixed on top of graphene and Au metal is deposited through the holes in mask by thermal evaporation method under vacuum condition. This fabrication method provides an easy, fast and cost efficiency way to generate periodical nanostructure. Also, Au nanoholes(NHs) structure has been studied by using holey Si₃N₄ as a template. The surface-enhanced Raman scattering (SERS) sensitivities of periodical Au NDs/graphene and graphene/Au NHs hybrid structures have been systematically studied. The internal mechanisms could be explained by chemical mechanism effect of graphene and electromagnetic mechanism effect of metallic nano-structures. The enhancement factors have been systematically investigated by varying the diameter and the thickness of Au discs and Au NHs. Raman mappings of Au NDs with 2.5 μm diameter illustrate that the larger SERS enhancements exist in the rim of NDs which has good agreement with the electric field simulation result. The SERE enhancement factors of fluorescein obtained from Au NDs/graphene substrates shows an improvement factor of 500% in comparison of graphene substrate. The calculated SERS enhancement factors of graphene/Au NHs achieve 1,200% in comparison of graphene/planar Au film substrate. .