We present a template-assisted fabrication method for a large-scale ordered arrays of ZnO nanorods (ZnO-NRs) modified with Ag nanoparticles (Ag-NPs), which possess high-density three-dimensional (3D) hot spots uniformly dispersed all over the substrate, being beneficial to ultrahigh sensitivity of surface enhanced Raman scattering (SERS) detection. These achieved Ag-NPs@ZnO-NRs arrays show high sensitivity, good spectral uniformity and reproducibility as substrates for SERS detection. Using the arrays, both dye molecules (rhodamine 6G, R6G) and organic pollutants like toxic pesticides (thiram and methyl parathion) are detected, with the detection limits of thiram and methyl parathion being 0.79*10-9 M and 1.51*10-8 M, respectively. In addition, the Ag-NPs@ZnO-NRs arrays have a self-cleaning function because the analyte molecules can be photocatalytic degraded using ultraviolet irradiation, showing that the 3D recyclable arrays have promising opportunities to be applied in rapid SERS-based detection of toxic organic pesticides.