Surface-enhanced Raman spectroscopy (SERS) stands out in the field of microbial analysis due to its rich molecular information, fast analysis speed, and high sensitivity. However, achieving strain-level differentiation is still challenging because numerous bacterial species inevitably have very similar SERS profiles. Here, a method inspired by the black-box theory was proposed to boost the spectral differences, where the undifferentiated bacteria was considered as a type of black-box, external environmental stress was used as the input, and the SERS spectra of bacteria exposed to the same stress was output. For proof of the concept, three types of environmental stress were explored, i.e., ethanol, ultraviolet light (UV), and ultrasound. Enterococcus faecalis (E. faecalis) and three types of Escherichia coli (E. coli) were all subjected to the stimuli (stress) before SERS measurement. Then the collected spectra were processed only by simple principal component analysis (PCA) to achieve differentiation. The results showed that appropriate stress was beneficial to increase the differences in bacterial SERS spectra. When sonication at 490 W for 60 s was used as the input, the optimal differentiation of bacteria at the species (E. faecalis and E. coli) and strain-level (three E. coli) can be achieved.