Vertically aligned Au decorated WO3 nanorods (Au-WO3 NRs) were investigated as cheap and sensitive surface-enhanced Raman scattering (SERS)-active substrates. The WO3 NRs were prepared through a simple, low-temperature hydrothermal route and made SERS-active through deposition of Au nanoparticles by ion sputtering. The structure and morphology of WO3 were investigated through XRD, SEM and TEM. The probe molecule rhodamine 6G (R6G) has been detected by using the substrate. It is found that the Au nanoparticles about 5 nm were uniformly distributed on the WO3 nanorod which has a rectangular cross-section. The Au-WO3 NRs substrate shows high sensitivity for R6G, suggesting a promising potential for application in rapid detection of environmental pollutants.