Ag nanoparticles (NPs) coated with silica nanolayers were decorated onto a large-scale and uniform silicon nanowire array (SiNWA) by simple chemical etching and metal reduction processes. The three-dimensional Ag/SiNWAs thus formed are employed as a substrate for surface-enhanced Raman scattering (SERS), and a detection limit for rhodamine 6G as low as 10(-16) M and a Raman enhancement factor as large as 10(14) were obtained. Simulation results show that two kinds of inter-Ag-NP nanogaps in three-dimensional geometry create a huge number of SERS 'hot spots' where electromagnetic fields are substantially amplified, contributing to the higher SERS sensitivity and lower detection limit. The excellent SERS stability of Ag/SiNWAs is attributed to the presence of the SiO2 nanolayer around Ag NPs that prevented the Ag NP surface from being oxidized. The calibration of the Raman peak intensities of rhodamine 6G and thiram allowed their quantitative detection. Our finding is a significant advance in developing SERS substrates for the fast and quantitative detection of trace organic molecules.