To perform the mechanism study of special association for vancomycin and D-Ala-D-Ala-containing peptides on the interface of solution and self-assemble monolayer, the binding between vancomycin and pentapeptide (Lys-Lys-Gly-D-Ala-D-Ala) was investigated by flow injection surface plasmon resonance (FI-SPR) and flow injection quartz crystal microbalance (FI-QCM). To facilitate the formation of a compact vancomycin adsorbates layer with a uniform surface orientation, vancomycin molecules were attached onto a preformed alkanethiol self-assembled monolayer. By optimizing the conditions for the binding between Lys-Lys-Gly-D-Ala-D-Ala and vancomycin on the assembled chip, the detecting limit of Lys-Lys-Gly-D-Ala-D-Ala was greatly improved (reaching 0.5 ×10^- 6 mol/L or 7.5 × 10^-12 mol). The equilibrium constant of the association of Lys-Lys-Gly-D-Ala-D-Ala with vancomycin was also obtained (KAds=5.0×10^4 L/tool).