Here, we report a label-free surface-enhanced Raman scattering (SERS) method for the rapid and accurate identification of methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) based on aptamer-guided AgNP enhancement and convolutional neural network (CNN) classification. Sixty clinical isolates of Staphylococcus aureus (S. aureus), comprising 30 strains of MSSA and 30 strains of MRSA were used to build the CNN classification model. The developed method exhibited 100% identification accuracy for MSSA and MRSA, and is thus a promising tool for the rapid detection of drug-sensitive and drug-resistant bacterial strains.