The identification of enantiomers is of great importance in chiral separations and medicinal chemistry. While Surface-enhanced Raman spectroscopy (SERS) is a technique that provides vibrational fingerprints of analytes. The enantiomers identification relies on the SERS difference between left and right-handed circularly polarized light or additional selectors for indirect distinction. In this work, Au–Ag core shell nanobipyramid (L/D-Au@Ag BPs) were synthesized guiding by chiral encoder of L/D-cysteine. L/D-Au@Ag BPs produced plasmon-induced circular dichroism signals in the plasmon resonance absorption band, which can be tuned by modulation the amount of cysteine. Moreover, the chiral anisotropy factor of L/D-Au@Ag BPs at 532 nm can reach 5.11 × 10−3. Due to the selective resonance coupling between L/D-Au@Ag BPs and different enantiomers, L/D-Au@Ag BPs were further used as SERS substrates for efficient discrimination of biologically relevant small molecules. Chiral Au@Ag BPs display the potential for chiral drug identification.