The purpose of this work is to develop a high-performance surface-enhanced Raman scattering (SERS) substrate with high light harvesting and SERS emitting efficiencies based on the principle of a plasmonic nano-antenna. A prism/Ag nanowell array was designed and constructed based on the Kretschmann configuration. Almost 100% of the incident light can be absorbed at the resonance angle. A strong electromagnetic (EM) field is generated in the near field along the rim and at the center of the nanowells by means of the localized energy of surface plasmons (SPs), resulting in the electric field being enhanced 300 times at the Ag surface. The co-enhancement of localized SPs and propagating SPs was achieved in this substrate. The plasmonic nano-antenna structure can also redirect the SERS, which benefits the SERS collection. The SERS sensitivity on this configuration was improved by about 40 times compared with that on a conventional Kretschmann configuration with a flat Ag film. This SERS substrate design with full consideration on the tuning of the EM field in the near field and SERS space distribution in the far field could give insight into the design of a new generation of SERS substrates.