Silicon inverted pyramids have been shown to exhibit superior SERS properties compared to ortho-pyramids, yet low-cost, simple preparation processes are lacking at present. This study demonstrates a simple method, silver-assisted chemical etching combined with PVP, to construct silicon inverted pyramids with a uniform size distribution. Two types of Si substrates for surface-enhanced Raman spectroscopy (SERS) were prepared via silver nanoparticles deposited on the silicon inverted pyramids by electroless deposition and radiofrequency sputtering, respectively. The experiments were conducted using rhodamine 6G (R6G), methylene blue (MB) and amoxicillin (AMX) molecules to test the SERS properties of the Si substrates with inverted pyramids. The results indicate that the SERS substrates show high sensitivity to detect the above molecules. In particular, the sensitivity and reproducibility of the SERS substrates with a denser silver nanoparticle distribution, prepared by radiofrequency sputtering, are significantly higher than those of the electroless deposited substrates to detect R6G molecules. This study sheds light on a potential low-cost and stable method for preparing silicon inverted pyramids, which is expected to replace the costly commercial Klarite SERS substrates.