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In this research, it reported a novel three-dimensional (3D) metallic hybrid system by introducing single-layer graphene (SLG) between silver nanoparticles (NPs) and silver nano-discs (NDs) arrays (Ag NPs/SLG/Ag NDs). By combining the plasmonic metallic nanostructures and the unique physical/chemical properties of graphene, Ag NPs/SLG/Ag NDs hybrid substrate was fabricated, and it exhibited extremely high surface-enhanced Raman scattering (SERS) performance. By tuning the diameter of Ag NDs, the SERS performance of Ag NPs/SLG/Ag NDs hybrid substrate has been systematically studied. The detection limit for rhodamine 6g (R6G) could reach the concentrations as low as 1 × 10-12 mol/L, and the average enhancement factor (EF) of the Ag NPs/SLG/Ag NDs substrate could reach 5.65 × 108. These advantages indicated that the Ag NPs/SLG/Ag NDs hybrid substrate could be regarded as a candidate for organic molecules detection under extremely low concentration. Besides, spatial Raman mapping of Ag NPs/SLG/Ag NDs with 2.5 μm diameter NDs showed the larger SERE signal existed around the rim of Ag NDs which was related to the localized surface plasmons. This phenomenon was contributed by a larger electromagnetic field which was tuned by Ag NPs and the edge of Ag NDs. This mechanism also has been confirmed by the electromagnetic simulation result.