Laser-induced periodic surface structures (LIPSS) have gained significant attention due to their ability to modify the surface morphology of materials at the micro-nanoscale and show great promise for surface functionalization applications. In this study, we specifically investigate the formation of LIPSS in silicon substrates and explore their impact on surface-enhanced Raman spectroscopy (SERS) applications. This study reveals a stepwise progression of LIPSS formation in silicon, involving three distinct stages of LIPSS: (1) integrated low-spatial-frequency LIPSS (LSFL) and high-spatial-frequency LIPSS (HSFL), (2) principally LSFL and, (3) LSFL at the edge of the irradiated spot, elucidating the complex interplay between laser fluence, pulse number, and resulting surface morphology. Furthermore, from an application standpoint, these high-quality multi-scale periodic patterns lead to the next step of texturing the entire silicon surface with homogeneous LIPSS for SERS application. The potential of LIPSS-fabricated silicon substrates for enhancing SERS performance is investigated using thiophenol as a test molecule. The results indicate that the Au-coated combination of LSFL and HSFL substrates showcased the highest enhancement factor (EF) of 1.38×106. This pronounced enhancement is attributed to the synergistic effects of localized surface plasmon resonance (LSPR) and surface plasmon polaritons (SPPs), intricately linked to HSFL and LSFL characteristics. These findings contribute to our understanding of LIPSS formation in silicon and their applications in surface functionalization and SERS, paving the way for sensing platforms.