Ease of deprotonation what is called acidity about sulfonic group of model molecules of perfluorosulfonic acid (PFSA) membrane and hydrocarbon (HC) membrane was focused on in this study. The deprotonation reaction of sulfonic group by water molecules were analyzed by density functional theory in low hydration levels. Target hydration levels were one to three. Calculation level was B3LYP/6-311+G(d,p). As a result, sulfonic group of model molecules of PFSA is deprotonated in hydration level three via low activation energy. In addition, deprotonated state (SO3- group, H3O+ and two water molecules) is more stable than the protonated state (sulfonic group and three water molecules). On the other hand, deprotonated state of model molecule of HC in hydration level three is unstable. In addition, activation energy is relatively high. Those properties indicate sulfonic group of HC membrane is relatively hard to deprotonate in comparison with PFSA membrane in the same hydration level.