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A three‐dimensional surface‐enhanced Raman scattering (SERS) substrate via the self‐assembly of properly sized Au nanoparticles in anodic aluminum oxide templates was designed and prepared. Au nanoparticles first underwent hydrophobic surface modification. Then, the hydrophobic Au nanoparticles self‐assembled, aggregated and formed many hot spots in the anodic aluminum oxide templates through a supramolecular interaction. We chose thiophenol as a probe molecule to evaluate the SERS enhancement ability of this three‐dimensional substrate. The enhancement factor was calculated to be 4.6 × 106 under the radiation of a 785‐nm laser. By further comparing SERS signals from different points on the same substrate, we confirmed that this substrate possessed good reproducibility and could be applied for SERS detection. Copyright © 2011 John Wiley & Sons, Ltd.