Highly ordered treelike Si/ZnO hierarchical nanostructures are successfully prepared in a large scale by combining two common techniques, viz., photolithography-assisted wafer-scale fabrication of Si nanopillars and bottom-up hydrothermal growth of ZnO nanorods. Silver nanoparticles are decorated onto the nanotrees by photochemical reduction and deposition. The Si/ZnO/Ag hybrid nanotrees are employed as SERS-active substrates, which exhibit good performance in terms of high sensitivity and good reproducibility. In addition to the SERS application, such ordered Si/ZnO arrays might also find potential applications in light-emitting diodes and solar cells.