Abstract We report a simple magnetron sputtering method to fabricate large-scale vertically aligned ZnO@Ag nanorods (NRs) arrays using aligned ZnO-NRs arrays as a template. Via changing the thickness of Ag film, the density of Ag nanoparticles (NPs) on the surface of ZnO-NRs arrays can be readily tuned. Due to synergistic and charge transfer (CT) effect of the adjacent Ag NPs and ZnO-NRs, the optimized ZnO@Ag-NRs arrays employing Ag film with 15 nm thickness show the best surface-enhanced Raman scattering (SERS) for 4-aminothiophenol (4-ATP). The considerable SERS enhancement of the 4-ATP is ascribed to the CT between the 4-ATP and Ag NPs through the ZnO-NRs. With the help of the valence band of ZnO, the photo-induced electrons from the Ag NPs can be transferred to the lowest unfilled orbital (LUMO) of 4-ATP, forming the so-called “donor-bridge-acceptor” system. The present research is not only beneficial to the development of ZnO-NRs arrays as a nontoxic, biocompatible, highly SERS active substrate, but also helpful to study the CT behavior between Ag and ZnO for optoelectronic chemistry.