The intermolecular interaction energies between a water molecule and four models of pendant chains for perfluorinated ionomers, such as CF3OCF2CF2SO3H, CF3OCF2CF2SO3−, CF3CF2CF2COOH, CF3CF2CF2COO−, were analyzed by using a molecular orbital calculation. In order to investigate a variety of configurations, five hundred random configurations that water and monomer contact at their van der Waals surfaces were generated for each system. We employed an empirical correction method for dispersion energy defined by the equation Edisp = −fd(R)C6R−6, so as to reduce the computational costs. The C6 coefficients of this equation were optimized to reproduce the energies obtained at the MP2/aug-cc-pVDZ level of calculations, and then overall intermolecular interaction energies (Eint = EHF + Edisp) were evaluated as a summation of Edisp and intermolecular interaction energy at the HF/aug-cc-pVDZ level (EHF). From these analyses, we obtained the following conclusions. (1) The ether oxygen in the pendant chain cannot bind with water strongly due to fluorination. (2) De-protonations of sulfonic and carboxylic acids extend the region where water molecules sufficiently bind with pendant chains, and this effect would cause rich water absorption when these pendant chains form membranes. Therefore, the degree of proton disassociation would be one of the key factors for the water sorption ratio and membrane morphology. (3) The binding energy of the optimized configuration for CF3CF2CF2COO− + H2O is about 2.5 kcal mol−1 larger than that for the CF3OCF2CF2SO3− + H2O system because of the larger electron negativities of the oxygen atoms on deprotonated carboxylic acid compared with those on the sulfonic acid.