This study presents the development of highly efficient Surface-Enhanced Raman Scattering (SERS) substrates through femtosecond (fs) laser processing of crystalline silicon (Si), resulting in mountain-like microstructures. These microstructures, when decorated with gold nanoparticles (Au NPs), exhibit remarkable SERS performance due to the creation of concentrated hotspots. The enhanced Raman signals originate from the excitation of localized surface plasmon resonance (LSPR) of the Au NPs and the multi-scale rough morphology of the Si substrates. Finite-element method simulations confirm the electromagnetic field enhancement in narrow gaps, supporting the experimental observations. The fabricated substrates show high uniformity, oxidation resistance, long-term stability, and exceptional reproducibility, making them ideal for molecular detection, especially in food safety applications. A remarkable enhancement factor (EF) of 1010 is attained in the detection of Malachite Green (MG), boasting a limit of detection (LoD) as low as 10−14 M. This underscores the immense potential of this technique for achieving highly sensitive and dependable SERS-based sensing capabilities.