Substrate materials with high sensitivity and storage stability are crucial for the practical analytical application of surface-enhanced Raman scattering (SERS) techniques. In this work, a SERS-active substrate (Si/Au@Ag/ZIF-67) was fabricated with a metal-organic framework (ZIF-67) on a plasmonic surface (Si/Au@Ag) via self-assembly. The as-prepared material combined the properties of the abundant hotspots of the Au@Ag nanoparticles and the excellent adsorption performance of ZIF-67 for organic molecules. The synergy leads to high sensitivity of the composite substrate with a low detection limit for 4-aminothiophenol (a typical Raman reporter molecule) down to 2.0 × 10-9 M and the analytical enhancement factor (AEF) of the SERS substrate is 3.4 × 106. Moreover, the substrates exhibited good repeatability, high reproducibility, and reliable stability due to the MOF coating. The SERS signal was stable after 60 days of storage at room temperature. Ultimately, the optimal Si/Au@Ag/ZIF-67 was applied as a SERS sensor to analyze thiram, and the results showed a linear concentration range from 10-7 to 10-5 M with good linearity (R2 = 0.9934). The recoveries of thiram in spiked apple juice were in the range of 95.7-102.3%, with relative standard deviations less than 4.3%. These results predict that the proposed SERS substrates may hold great potential for the detection of environmental and food pollution in practical applications.