<p> A&#xa0;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 <i>S. aureus</i> 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, <i>S. aureus</i> can be detected with high sensitivity, achieving a low limit of detection of 1.009&#xa0;CFU/mL and a broad linear detection range from 10 to 10⁷&#xa0;CFU/mL. Additionally, <i>S. aureus</i> 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 <i>S. aureus</i> in milk products, and exhibits excellent practical applicability as well as potential application value in food safety.</p> Graphical abstract <p></p>