This work reports the gold-coated self-organized silicon nanopyramidal array prepared by a wet etching and magnetron sputtering process at room temperature. Scanning electron microscopy was used to detect the morphology of gold films. The surface-enhanced Raman scattering (SERS) spectra of the rhodamine 6G (R6G) molecules adsorbed on a nanoscale gold film were recorded. Experimental results show the relationships between gold film thickness and SERS intensity. A full three-dimensional finite difference time domain calculations were carried out, which compare the experimental results and show agreement with ratios of the SERS enhancement for the different thicknesses of gold films. Furthermore, numerical simulations of the array were conducted for both a real gold metal coating and a perfect electrical conductor to determine whether the SERS enhancement was due to diffraction or plasmonic effects. The sample with the fast fabrication process used in this work could provide a new way to obtain a uniform enhancement and low cost SERS substrate.