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Large scale and highly ordered flowerlike ZnO/Si nanostructures are successfully prepared by combining two common techniques, viz. hydrothermally etch fabrication of nanoporous Si pillar array (NSPA) and self-catalytic chemical vapor transport growth of ZnO nanowires. Au nanoparticles are decorated onto the ZnO/Si nanoflowers by the hydrothermal method. The formed Au/ZnO/NSPA array is evaluated as a surface-enhanced Raman scattering SERS-active substrate, which exhibits very high sensitivity and good stability and reproducibility. The excellent SERS enhancement is mainly attributed to the strong local electromagnetic effect which is associated with the unique flowerlike nanostructures of Au/ZnO/NSPA and the formed metal-induced gap states at the Au/ZnO interfaces. The results indicated that Au/ZnO/NSPA might be employed as a promising SERS substrate for the fast detection of low-concentration biomolecules.