In this study, we fabricated four different structures using single crystal silicon wafers for surface-enhanced Raman spectroscopy (SERS) applications. For single crystal silicon, different crystal orientations exhibit different physical and chemical properties. In chemical etching, the etching speed of different crystal planes also exhibits significant differences. We first used reactive ion etching (RIE) to process the surface of the substrate, and subsequently used KOH anisotropic wet etching technology to modify the surface of silicon wafers with different crystal orientations and produced four different results. In the RIE stage in an O2 atmosphere, the (110) silicon wafer formed a hexagonal hole structure, and the (100) silicon wafer formed an inverted pyramid hole structure; however, in the RIE-treated substrates in O2 and SF6 atmosphere, the (110) silicon wafer formed a pyramid with a diamond-shaped base, and the (100) silicon wafer showed a columnar structure with a "straw hat" at the top. The formation mechanisms of these four structures were elucidated. We also performed structure-related SERS characterizations of the four different structures and compared their performance differences.