In this work, an innovative and simple growth approach of two-step solid state dewetting (SSD) has been introduced for the fabrication of bimetallic and core-shell nanoparticle (NP) configurations. A significant surface-enhanced Raman spectroscopy (SERS) enhancement on the hybrid Pd@Ag core-shell NP substrate is systematically demonstrated by a unique hybrid approach of mixing the graphene quantum dots (GQDs) and Rhodamine 6G (R6G). Due to the substantially increased electromagnetic hotspots in the hybrid Pd@Ag core-shell NP configuration and also the charge transfer enhancement by the addition of GQDs through the chemical enhancement mechanism, over 100 times of SERS signal enhancement is observed for the detection of R6G. The hybrid Pd@Ag core-shell NPs with the background Ag NPs and fully alloyed bi-metallic AgPd NPs without the background Ag NPs are demonstrated on sapphire (0001). The bimetallic and core-shell NPs demonstrate much enhanced localized surface plasmon resonance (LSPR) and thus significantly improved SERS responses. In specific, the hybrid Pd@Ag core-shell NPs demonstrate a gradual blue-shift and narrowing of LSPR peaks while the fully alloyed bi-metallic AgPd NPs show a continuing redshift and broadening of LSPR peaks.