Surface-enhanced Raman scattering (SERS) is a powerful technique for detecting trace heavy metal ions due to its non-destructiveness, high sensitivity and fast acquirement of the signal. Localized surface plasmon resonance (LSPR) is well known to enhance the electromagnetic field by reducing the gaps between plasmonic metal nanoparticles, which could greatly increase SERS performance. Recently, a new emerging route is more attractive, which can effectively enhance SERS by boosting the coupling between LSPR and surface plasmon polariton (SPP) through designing specific 3D nanostructures. Herein, we proposed a novel configuration of high-performance SERS chips with 3D periodic metal/dielectrics nanostructures, which can be fabricated in large areas and batches using nanoimprint lithography (NIL) based on a new concept of the stress-homogenized dual-layer template. The SERS chips fabricated using low-cost NIL were successfully applied to detection trace mercury (Hg) ions. The combination of theory and experiments allows a methodology for designing stress-homogenized nanoimprinting templates with vertical configuration and horizontal dimension as the key design parameters. The simulation of micro-/nano-scale interfacial stress evolution during NIL using finite element analysis (FEA) showed the formation of both high and low-stress sub-areas on a patterned template by introducing an extra structure layer normal to the template. Compared to the extra-layer free template, the area with high stress is about 72% that of the patterned area, accompanied by 17% improvement in stress distribution uniformity. A stress area as low as about 28% surrounding the patterned structure is also favorable for demolding during NIL. The horizontal dimension of the template was also revealed to have a dramatic effect on the micro-/nano-scale interfacial stress in whichreducing the size of the template would increase the overall interface stress significantly by one to two orders of magnitude. Various nanoimprint templates with different configurations and dimensions were employed to successfully nanoimprint large area and uniform dielectric nanostructures, demonstrating the stress homogenization proposed based on the simulations. We combined Au nanoparticles, and nanoimprint lithography resists to form the 3D periodic nanostructures of SERS chips. The SERS chips realized the detection limit for Rhodamine 6G (R6G) model molecule of 2.08×10^-12 mol·L^-1, an enhancement factor (EF) of up to 3×10⁸, and a uniformity of 8.07%. Furthermore, the SERS chips were also successfully applied to detect trace Hg ions as low as 5.0×10^-11 mol·L^-1 (10 ppt) with a good linear relationship (R²=0.966) ranging from 5.0×10^-11 to 5.0×10^-5 mol·L^-1, which is quite prominent for Hg ions detection. The SERS chips designed and fabricated here can provide a solution to trace detection of heavy metal ions and other trace substances. The concept of stress-homogenized dual-layer template proposed in this work makes it possible to fabricate high-performance, uniform and low-cost SERS chips with 3D nanostructures. The roadmap proposed in this study will undoubtedly promote greatly practical applications of SERS probes from the perspectives of both design and low-cost and batchable fabrication.