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In this work, we designed and prepared a hierarchically assembled 3D plasmonic metal-dielectric-metal (PMDM) hybrid nano-architecture for high-performance surface-enhanced Raman scattering (SERS) sensing. The fabrication of the PMDM hybrid nanostructure was achieved by the thermal evaporation of Au film followed by thermal dewetting and the atomic layer deposition (ALD) of the Al₂O₃ dielectric layer, which is crucial for creating numerous nanogaps between the core Au and the out-layered Au nanoparticles (NPs). The PMDM hybrid nanostructures exhibited strong SERS signals originating from highly enhanced electromagnetic (EM) hot spots at the 3 nm Al₂O₃ layer serving as the nanogap spacer, as confirmed by the finite-difference time-domain (FDTD) simulation. The PMDM SERS substrate achieved an outstanding SERS performance, including a high sensitivity (enhancement factor, EF of 1.3 × 10⁸ and low detection limit 10⁻¹¹ M) and excellent reproducibility (relative standard deviation (RSD) < 7.5%) for rhodamine 6G (R6G). This study opens a promising route for constructing multilayered plasmonic structures with abundant EM hotspots for the highly sensitive, rapid, and reproducible detection of biomolecules.