In this study, affinity capillary electrophoresis (ACE) and quantum mechanical density functional theory (DFT) calculations were combined to investigate non-covalent binding interactions between the hexaarylbenzene-based receptor (R) and alkali metal ions, Rb+ and Cs+, in methanol. The apparent binding (stability) constants (K-b) of the complexes of receptor R with alkali metal ions in the methanolic medium were determined by ACE from the dependence of effective electrophoretic mobility of the receptor R on the concentration of Rb+ and Cs+ ions in the BGE using a non-linear regression analysis. The receptor R formed relatively strong complexes both with rubidium (log K-b = 4.04 +/-0.21) and cesium ions (log K-b = 3.72 +/- 0.22). The structural characteristics of the above alkali metal ion complexes with the receptor R were described by ab initio density functional theory calculations. These calculations have shown that the studied cations bind to the receptor R because they synergistically interact with the polar ethereal fence and with the central benzene ring via cation-pi interaction.