Herein, we report an efficient method to produce silver (Ag) nanoparticle-decorated silicon (Si) nanowire (NW) arrays on a pyramidal Si (P-Si) substrate by using a pure chemical method and rapid thermal annealing in different atmospheres. A metal-assisted chemical etching technique was used to produce vertical Si NW arrays on pyramidal Si. The etching was observed to be heavily dependent on the substrate type. On planar Si (100), the etching was observed to occur in a uniform manner. However, the etching rate was observed to increase from the top to the base of the Si pyramid. The Si NWs produced from P-Si have zig-zag sidewalls as observed from high-resolution transmission electron microscopy images. However, for the same oxidant concentration, Si NWs produced from planar Si (100) consist of straight and amorphous sidewalls. Local variation of oxidant concentration is responsible for the formation of different sidewalls. The substrates are both surface-enhanced Raman scattering (SERS) active and hydrophobic. The hydrophobicity is due to the dual scale of roughness contributed to by both pyramidal and NW structures. Finite-difference time-domain simulation shows that the gap between two Ag spheres and also the gap between Si NWs and Ag spheres contributed to SERS enhancement.