A reliable and sensitive sensing of multiple foodborne pathogens is critical for timely diagnosis and human health. To meet this need, herein, we designed a sandwich immunoassay platform, using functionalized SERS probes and magnetic beads, for the interference-free simultaneous detection of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) in food samples by surface-enhanced Raman scattering (SERS) technology. The signal of two SERS probes coded by triple bonds (CC and CN) located at 2105 and 2227 cm⁻¹, respectively, could perfectly avoid the spectral overlap with coexisting materials in the Raman fingerprint region, which ensured the accuracy of the immunoassay platform. The application of functional magnetic beads, integrating enrichment and separation, greatly improved the sensitivity of the detection system. Under magnetic force, due to the mature interaction between the antigen and antibody, the sandwich immunoassay platform could be fabricated. Its limit of detection (LOD) for the simultaneous detection of E. coli and S. aureus was as low as 10 and 25 cfu mL⁻¹, respectively, and the sandwich immunoassay platform was successfully applied for the detection of E. coli and S. aureus in bottled water and milk. As a sensitive and highly selective analytical technique for the simultaneous multiple detection of pathogens, this SERS-based method has great potential to be applied in the field of food safety.