A new, highly sensitive and uniform three-dimensional (3D) hybrid surface-enhanced Raman scattering (SERS) substrate has been achieved via simultaneously assembling small Ag nanoparticles (Ag-NPs) and large Ag spheres onto the side surface and the top ends of large-scale vertically aligned cone-shaped ZnO nanorods (ZnO-NRs), respectively. This 3D hybrid substrate manifests high SERS sensitivity to rhodamine and a detection limit as low as 10−11 M to polychlorinated biphenyl (PCB) 77—a kind of persistent organic pollutants as global environmental hazard. Three kinds of inter-Ag-NP gaps in 3D geometry create a huge number of SERS “hot spots” that mainly contribute to the high SERS sensitivity. Moreover, the supporting chemical enhancement effect of ZnO-NRs and the better enrichment effect ascribed to the large surface area of the substrate also help to achieve a lower detection limit. The arrays of cone-shaped ZnO-NRs decorated with Ag-NPs on their side surface and large Ag spheres on the top ends have potentials in SERS-based rapid detection of trace PCBs.