Insights into the chemical essence of weak interactions on the surface of biomacromolecules may help to regulate biological processes. In this work, the pH sensitivity of ion-pair interactions occurring on a cysteine self-assembled monolayer (Cys SAM) that simulates the local surface of a protein was probed by scanning electrochemical microscopy (SECM). Cys SAM and the ion-pair interactions subsequently formed with the introduced aspartic acid (Asp) were both pH-sensitive, as confirmed by the tip current changes in the feedback mode. After continuous pH measurements, the most significant negative feedback was observed at pH 5.50, indicating the most robust ion-pair interactions, which were simultaneously identified by voltammetry. In this case, the extra addition of the inorganic cation (i.e., Ca2+) did not disrupt the existing ion-pair interactions, and the binding constant (K) and Gibbs free energy (ΔGo) of the ion pair were finally determined to be 6.44 × 105 M-1 and -33.14 kJ mol-1, respectively. Overall, the pH sensitivity of ion-pair interactions was found to be mainly attributable to pH-induced changes in the deprotonated/protonated states of the α-amino acid moieties, which may provide insights into the artificial manipulation of complex binding events at the molecular level on the biological surface.