The hazard of Hg ion pollution triggers the motivation to explore a fast, sensitive, and reliable detection method. Here, we design and fabricate novel 36-nm-thick Ag–Au composite layers alteately deposited on three-dimensional (3D) periodic SiO2 nanogrids as surface-enhanced Raman scattering (SERS) probes. The SERS effects of the probes depend mainly on the positions and intensities of their localized surface plasmon resonance (LSPR) peaks, which is confirmed by the absorption spectra from finite-difference time-domain (FDTD) calculations. By optimizing the structure and material to maximize the intrinsic electric field enhancement based on the design method of 3D periodic SERS probes proposed, high performance of the Ag–Au/SiO2 nanogrid probes is achieved with the stability further enhanced by annealing. The optimized probes show the outstanding stability with only 4.0％SERS intensity change during 10-day storage, the excellent detection uniformity of 5.78％(RSD), the detection limit of 5.0×10?12 M (1 ppt), and superior selectivity for Hg ions. The present study renders it possible to realize the rapid and reliable detection of trace heavy metal ions by developing high-performance 3D periodic structure SERS probes by designing novel 3D structure and optimizing plasmonic material.