Nanostructures and nanoparticles are two typical structures which have already been widely employed as the Surface Enhanced Raman Scattering (SERS) substrates. In most studies, they are employed separately as SERS substrates. Recently, the hierarchical structures including nanostructures and nanoparticles present better SERS characteristics. However, how to machine such hierarchical structures is a big problem. In the present study, a novel method integrating the nanoindentation process and chemical redox reaction to machine the hierarchical SERS substrate is provided. Micro/nanostructures are formed on the Cu(110) plane first, and then Ag nanoparticles are generated on the structured Copper surface. Effects of parameters of the indentation process and the corrosion times in the AgNO3 solutions on the Raman intensities of the SERS substrate with hierarchical structures are experimentally studied. The intensity and distribution of the electric field of single and multi Ag nanoparticles on the surface of plane and micro/nanostructures are studied with the COMSOL software. The feasibility of the hierarchical SERS substrate is verified using R6G molecules. Finally, the enhancement factor of malachite green molecules can reach to 5.089×109, which proves that the method is simple, replicable and low cost method for machining the hierarchical SERS substrate.