A novel recyclable SERS substrate with magnetic manipulation capability and surface-enhanced Raman scattering (SERS) effect based on Fe3O4@PEI-DTC-Au@Ag (FPDAA) core-shell nanocomposites has been successfully prepared by engineered hydrothermal deposition and seed deposition techniques. The uniformity and SERS efficacy of these substrates, incorporating various Au@Ag core-shell nanocomposites with differing Ag shell thicknesses, were evaluated using 4-aminothiophenol (4-ATP) molecules. The optimal SERS substrate, Fe3O4@PEI-DTC-Au@Ag-3 (FPDAA-3), exhibited an enhancement factor (EF) of up to 1.121×106. This remarkable performance can be attributed to the synergistic effect between the magnetic plasmon of the Fe3O4 nanoparticles (NPs) core and the surface plasmonic resonance properties of Au@Ag core-shell nanocomposites, which create abundant interparticle hotspots within the FPDAA nanocomposites. Furthermore, the FPDAA-3 nanocomposite was employed as a SERS substrate for rapid thiram detection, achieving a minimum detectable concentration of 1×10−9 M. Notably, the relative standard deviation of SERS measurements from 50 randomly selected points was found to be less than 12.13 %, and the SERS spectra intensity showed minimal variation after 5 cycling tests, underscoring the excellent uniformity and recyclability of the FPDAA-3 substrate. The highly reusable and reliable FPDAA-3 nanocomposites enable direct on-site detection of thiram pesticide residues on fruit skins, thereby offering significant implications for food safety assessment and spectroscopic identification.