Calixarenes are macrocyclic oligomers having the shape of a conical vase. Their inner cavity can accommodate various guest molecules, i. e. form supramolecules. Thus, calixarenes can be employed to manipulate selectivity in separation sciences. The essential step of separation is the interaction between calixarene and analytes. Therefore, in the present work, the retention mechanisms of benzenediol and naphthol positional isomers on a calix[4]arene column were investigated. The optimized supramolecular structures showed that there exist hydrogen bonding and pi-pi interactions for benzenediol, and for naphthol the pi-pi interactions dominate. Thermodynamic results from quantum chemistry calculations using DFT-B3LYP/STO-3G** basis set were consistent with the retention behaviors of benzenediol and naphthol positional isomers on the calix[4]arene column. This work will provide theoretical support for the design of new calixarene stationary phases.