The binding modes, inclusion abilities, and thermodynamic parameters for the intermolecular complexation of p-sulfonatocalix[4]arene (SC4A), p-sulfonatocalix[5]arene (SC5A), and p-sulfonatothiacalix[4]arene (STC4A), with methyl viologen (MV(2+)), ethyl viologen (EV(2+)), propyl viologen (PV(2+)), butyl viologen (BV(2+)), and benzyl viologen (BnV(2+)), were systematically investigated by NMR spectroscopy, molecular mechanics calculation, and microcalorimetry in neutral aqueous solutions. The obtained results show that all the sulfonated calixarene hosts can form stable inclusion complexes with viologen guests driven by much favorable enthalpy changes. All the viologen guests are encapsulated into the smaller SC4A cavity in their axial orientation. The larger SC5A cavity can accommodate all the viologen guests at its upper-rim midsection in the latitudinal orientation. The binding modes of more flexible STC4A with the smaller MV(2+) and EV(2+) guests are similar to those of SC5A with the two guests, while the binding modes of STC4A with the larger PV(2+) and BV(2+) guests are similar to those of SC4A with the two guests. The host selectivity for all the investigated viologen guests is the same: SC5A > SC4A > STC4A. The magnitude of the host selectivity is associated with the size of the guest. Moreover, the thermodynamic origin of the host selectivity for these viologen guests can be explained well by host-guest binding modes.