Using a patterned sapphire substrate with a hemisphere array, flower-like ZnO nanorods grouped in a highly ordered array were fabricated on the wafer scale by routine solution growth. After decorating with high-density Ag nanoparticles (NPs), the ZnO nanoflower arrays were used as the substrates for surface enhanced Raman scattering (SERS). Using Rhodamine 6G as the probe molecules with a concentration down to 10⁻¹⁰ M, the SERS substrates present an as high as 10¹⁰ Raman enhancement with good reproducibility. The influence of Ag NP decoration on the SERS activity was explored and the sub-10 nm nanogaps between the adjacent Ag NPs were proved to be the primary electromagnetic “hot spots” responsible for the significant Raman enhancement. The Ag-NP-decorated ZnO nanoflower arrays were demonstrated to possess a self-cleaning function enabled by UV irradiation via photocatalytic degradation of the analyte molecules. In addition, the SERS substrate exhibited an extremely long service lifetime, possibly due to its superhydrophobicity and storage in the dark and a dry environment.