A new family of aryl-extended calix[4]pyrroles with two phoshonate groups can act as ion-pair receptors for guests alkylammonium/phosphonium chloride salts, and the ion-pair binding mode and binding affinity of these hosts are different. In the present contribution, the origin of opposite ion-pair binding behavior for two typical hosts ii and oo towards primary ammonium chloride salt and quaternary phosphonium chloride salt was investigated using quantum mechanics (QM) calculations and new nonconvalent weak interaction analysis method. Two types of arrangements – separated and contact – were taken into account for each complex. The binding energy suggests that contact and separated arrangements is the favorable binding mode for receptor ii and oo respectively. Furthermore, the primary alkylammonium chloride salt binds stronger to ii than to oo, while quaternary phosphonium chloride salt binds stronger to oo than to ii, in agreement with the experiment. Moreover, geometry, charge transfer based on natural bond orbital (NBO) and nonconvalent weak interactions analysis suggest that the hydrogen bonding and cation–π interactions play the critical role in ion-pair recognition of ii and oo respectively due to the different orientation of the P=O groups. This work further unveils the mechanism of ion-pair recognition by new calix[4]pyrrole bis-phosphonate receptors, while opening exciting perspectives for the design of stronger and more efficient calix[4]pyrrole-based ion-pair receptors.