Graphene/noble metal substrates for surface enhanced RAMAN scattering (SERS) possess synergistically improved performance, due to the strong chemical enhancement mechanism accounted to graphene and the electromagnetic mechanism raised from the metal nanoparticles. However, only the effect of noble metal nanoparticles characteristics on the SERS performance was studied so far. In attempts to bring a light to the effect of quality of graphene, in this work, two different graphene oxides were selected, slightly oxidized GOS (20%) with low aspect ratio (1000) and highly oxidized (50%) GOG with high aspect ratio (14,000). GO and precursors for noble metal nanoparticles (NP) simultaneous were reduced, resulting in rGO decorated with AgNPs and AuNPs. The graphene characteristics affected the size, shape, and packing of nanoparticles. The oxygen functionalities actuated as nucleation sites for AgNPs, thus GOG was decorated with higher number and smaller size AgNPs than GOS. Oppositely, AuNPs preferred bare graphene surface, thus GOS was covered with smaller size, densely packed nanoparticles, resulting in the best SERS performance. Fluorescein in concentration of 10−7 M was detected with enhancement factor of 82 × 104. This work demonstrates that selection of graphene is additional tool toward powerful SERS substrates.