Surface-enhanced Raman scattering (SERS) enables pesticide residue monitoring to become facile and efficient. In this study, a core–shell structured gold nanoparticles@ZnCo metal–organic framework (AuNPs@ZnCo-MOF) SERS substrate was designed and successfully synthesized for efficient and selective detection of thiram. The bimetallic ZnCo-MOF shell can not only enrich the targeted molecules in the electromagnetic field because of its excellent absorptive capacity, but also act as a stabilized matrix for protecting the AuNPs from aggregation. The AuNPs@ZnCo-MOFs exhibited a high enhancement factor (EF) of 3.51 × 10⁶ and a low detection limit of 1 × 10⁻⁷ mol L⁻¹. Besides, the substrate material showed exceptional stability for up to 28 days at room temperature. The AuNPs@ZnCo-MOFs were used to detect thiram which displayed wide linearity (1 × 10⁻⁷ to 1 × 10⁻⁴ mol L⁻¹) and high recoveries (83.45–99.61%). Moreover, the AuNPs@ZnCo-MOF SERS substrate exhibited excellent anti-interference ability and size selectivity for the target molecules. These indicate that the AuNPs@ZnCo-MOF substrate has great potential for the detection of thiram residues in practical applications.