Accurate design of high‐performance 3D surface‐enhanced Raman scattering (SERS) probes is the desired target, which is possibly implemented with a prerequisite of quantifying formidable multiple coupling effects involved. Herein, by combining theory and experiments on 3D periodic Au/SiO2 nanogrid models, a generalized methodology of accurately designing high performance 3D SERS probes is developed. Structural symmetry, dimensions, Au roughness, and polarization are successfully correlated quantitatively to intrinsic localized electromagnetic field (EMF) enhancements by calculating surface plasmon polariton (SPP), localized surface plasmon resonance (LSPR), optical standing wave effects, and their couplings theoretically, which is experimentally verified. The hexagonal SERS probes optimized by this methodology realize over two orders of magnitudes (405 times) improvement of detection limit for Rhodamine 6G model molecules (2.17 × 10−11 m) compared to the unoptimized probes with the same number density of hot spots, an enhancement factor of 3.4 × 108, a uniformity of 5.52%, and are successfully applied to the detection of 5 × 10−11 m Hg ions in water. This unambiguously results from the Au roughness‐independent extra 144% contribution of LSPR effects excited by SPP interference waves as secondary sources, which is very unusual to be beyond the conventional recognition.
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