A multifunctional surface-enhanced Raman scattering (SERS) sensor was initially developed by integrating MXene with Au nanoparticles (MXene/Au) and plasmonic metal composite (Au@Ag NFs) as the substrate, combined with aptamers (apt) and signal molecules (4-MBA) for sensitively recognizing S. aureus in milk products. Firstly, MXene possesses the characteristic of a large specific surface area. On the one hand, it provides a higher number of attachment sites for the plasmonic metal composite, enabling the metal nanoparticles to be uniformly distributed on its surface. On the other hand, it exhibits a pre-enrichment effect for the target bacteria, remarkably enhancing the sensitivity of the SERS sensor. Secondly, Au@Ag NFs/4-MBA coupled with MXene/Au produced a synergistic electromagnetic (EM) enhancement effect, which greatly enhanced the SERS intensity and amplified the Raman signal. Furthermore, the thiol-modified aptamer (SH-apt) dramatically enhances the specificity of the SERS sensor system. Based on the sandwich-structured MXene/Au-apt-Au@Ag NFs/4-MBA, S. aureus can be detected with high sensitivity, achieving a low limit of detection of 1.009 CFU/mL and a broad linear detection range from 10 to 10 CFU/mL. Additionally, S. aureus in milk products can be detected with satisfactory recoveries of 86.38-106.65%, which indicates that it has good practical applicability. This method provides an innovative SERS strategy for rapidly monitoring S. aureus in milk products, and exhibits excellent practical applicability as well as potential application value in food safety.