A sensitive and stable substrate plays a vital role in the Raman spectroscopic techniques as an analytical method for detecting pesticides effectively from the environment. Enhancing signals from nanoparticles are weak and inconsistent in repeatability since analytes tend to degrade quickly under laser exposure. Herein, a novel substrate of Au@ZIF-67 is prepared on octahedral AuNPs by trapping pesticide molecules with small three-dimensional volumes by the flexibility of ZIF-67 for rapid detection with high sensitivity and stability. The two types of thiram and carbendazim pesticides, which are environmental pollutants that affect biodiversity, were successfully absorbed in Au@ZIF-67 nanostructures by adsorption-desorption equilibrium for analytical purposes in Raman spectroscopy. Spectra calculations of the thiram and carbendazim molecules on 8 atoms of Au using DFT were compared with the experimental data. The SERS enhancement factors for thiram and carbendazim were estimated to be 1.91 × 10⁸ and 3.12 × 10⁸, respectively, with the LOD values of trace amounts of ∼10⁻¹⁰ mol L⁻¹. The novel substrate of Au@ZIF-67 is a propitious platform for detecting thiram and carbendazim in trace amounts, providing a helpful strategy for detecting residues with high performance in the environment at the laboratory and practical scales.