Rapid and effective detection of pesticide residues from complex surfaces of fruits and vegetables has important significance. Herein, we report a novel three-dimensional (3D) hierarchical porous functional surface-enhanced Raman scattering (SERS) substrate, which is fabricated by successive two-step hydrothermal synthesis strategy of silver nanoparticles (Ag NPs) and cobalt oxide nanowires (Co3O4 NWs) on the 3D copper foam framework as Cu@Co3O4@Ag-H. The strategy offers a new avenue for localized plasmonic materials distribution and construction, which exhibits better morphology regulation ability and SERS activity (or hotspots engineering) than physical spurring obtained Cu@Co3O4@Ag-S. The developed Cu@Co3O4@Ag-H possesses large surface area and rich hotspots, which contributes to the excellent SERS performance, including homogeneity (RSD of 7.8%), sensitivity (enhancement factor, EF of 2.24 × 108) and stability. The Cu@Co3O4@Ag-H not only provides plenty of Electromagnetic enhancement (EM) hotspots but also the trace detection capability for droplet rapid sensing within 2 s. Cu@Co3O4@Ag-H substrate is further developed as an effective SERS sensing platform for pesticide residues detection on the surfaces of fruits and vegetables with excellent LOD of 0.1 ppm, which is lower than the most similar reported works. This work offers new potential for bioassay, disease POCT diagnosis, national security, wearable flexible devices, energy storage and other related fields.