Surface-enhanced Raman scattering (SERS) have numerous applications in areas such as analytical chemistry, biochemistry, and environmental science. However to manufacture SERS active substrates with good reproducibility and low cost is not easy, which hinder the SERS technology from being widespread in various applications. In this study, we developed a batch producible hot embossing 3D nanostructured SERS substrate technology for SERS applications. This study utilized the anodic aluminum oxide (AAO) self-assembled uniform nano-hemispherical array barrier layer as a template to create a durable nanostructured nickel mold. With the hot embossing technique and the durable nanostructured nickel mold, we were able to batch produce the 3D Nanostructured SERS chip with consistent quality and low cost. In addition, according to the SERS experiments, the 3D nano-hemispherical cavity array combined with sub-10-nm-gaps Au NPs showed distinct SERS signals in both Rhodamine 6G and Chlorpyrifos measurements. Therefore, the developed method is good to be used extensively in rapid chemical and biomolecular detection applications.