Various sizes and morphologies of noble metal/zinc oxide hybrid materials have promising applications in surface-enhanced Raman scattering (SERS). Generally, organic agents used during the synthesis of metal nanoparticles will inexorably induce organic pollution on the surface of SERS substrate, resulting in a negative effect on detection sensitivity. Herein, a stable and clean 3D flower-like ZnO/Ag hierarchical microstructure SERS substrate was designed and fabricated via a simple photocatalytic method. This synthetic strategy does not involve usage of any organic agents, which ensures the cleanness and free of impurities interferences. As anticipated, the as-fabricated 3D flowerlike ZnO/Ag SERS substrates with high surface-to-volume ratio increased numerous hot spots, and exhibited excellent detection sensitivity to Rhodamine 6G. A linear relationship between the Raman intensity and the concentration of Rhodamine 6G ranging from 10 −11 to 10 −4 M was realised. This work demonstrated a performance-enhanced SERS sensor based on microflower-like ZnO@Ag hybrids, which provides a potential method to develop highly sensitive and stable SERS sensor for organic molecules detection.