Surface-enhanced Raman scattering (SERS) is a powerful analytical technique for chemical identification, but it remains a great challenge to realize the large-scale and well-controlled fabrication of sensitive and repeatable SERS substrates. Here, we report a facile strategy to fabricate centimeter-sized periodic Au nanograting (Au-NG) decorated with well-arranged Ag nanoparticles (Ag-NPs) (denoted as Ag-NPs@Au-NG) as a three-dimensional (3D) flexible hybrid SERS substrate with high sensitivity and good reproducibility. The Au-NG patterns with periodic ridges and grooves are fabricated through nanoimprint lithography by employing a low-cost digital versatile disc (DVD) as a master mold, and the Ag-NPs are assembled by a well-controlled interface self-assembly method without any coupling agents. Multiple coupling electromagnetic field effects are created at the nanogaps between the Ag-NPs and Au-NG patterns, leading to high-density and uniform hot spots throughout the substrate. As a result, the Ag-NPs@Au-NG arrays demonstrate an ultrahigh SERS sensitivity as low as 10-13 M for rhodamine 6G with a high average enhancement factor (EF) of 1.85 × 108 and good signal reproducibility. For practical applications, toxic organic pollutants including crystal violet, thiram, and melamine have been successfully detected with high sensitivity at a low detection limit, showing a good perspective in the rapid detection of toxic organic pollutants.