Fabricating perfect plasmonic nanostructures has been a major challenge in surface enhanced Raman scattering (SERS) research. Here, a double-layer stacked Au/Al2O3@Au nanosphere structures is designed on the silicon wafer to bring high density, high intensity “hot spots” effect. A simply reproducible high-throughput approach is shown to fabricate feasibly this plasmonic nanostructures by rapid thermal annealing (RTA) and atomic layer deposition process (ALD). The double-layer stacked Au nanospheres construct a three-dimensional plasmonic nanostructure with tunable nanospacing and high-density nanojunctions between adjacent Au nanospheres by ultrathin Al2O3 isolation layer, producing highly strong plasmonic coupling so that the electromagnetic near-field is greatly enhanced to obtain a highly uniform increase of SERS with an enhancement factor (EF) of over 107. Both heterogeneous nanosphere group (Au/Al2O3@Ag) and pyramid-shaped arrays structure substrate can help to increase the SERS signals further, with a EF of nearly 109. These wafer-scale, high density homo/hetero-metal-nanosphere arrays with tunable nanojunction between adjacent shell-isolated nanospheres have significant implications for ultrasensitive Raman detection, molecular electronics, and nanophotonics.