Surface-enhanced Raman spectroscopy (SERS) substrates based on gold nanoparticles (AuNPs) typically suffer from limited enhancement efficiency due to random AuNPs aggregation. This aggregation issue, however, can be resolved by synthesizing AuNPs using cyclodextrin metal-organic framework (CD-MOF) as a structural template-a strategy that suppresses aggregation and yields well-defined Au@CD-MOF composites with enhanced SERS-active structures. Additionally, glycerol triglycidyl ether (GTE) was introduced as a cross-linking agent to address the high water sensitivity of Au@CD-MOF. The cross-linked product (CL-Au@CD-MOF) exhibited excellent SERS reproducibility and remarkable stability. The CL-Au@CD-MOF exhibited an exceptional enhancement factor (EF) of 2.32 × 10 and achieved a remarkable minimum detectable concentration of 2.7 × 10 M for malachite green (MG) in both aqueous and acetonitrile solutions. Furthermore, loading CL-Au@CD-MOF onto polydimethylsiloxane (PDMS)-coated filter paper (FP) yielded a composite substrate (CL-Au@CD-MOF/PDMS-FP) with superior SERS performance. This substrate exhibited excellent reproducibility, broad temperature adaptability, and robust storage stability. These favorable properties enable the sensitive detection of thiabendazole and thiram residues in apple and cucumber samples. These findings highlight the versatility and stability of CD-MOF-based composites, positioning them as highly effective platforms for detecting diverse substances and underscoring their great potential in food safety applications.