We present a theoretical study on the proton dissociation properties of the membranes for polymer electrolyte fuel cells. A density functional theory method is used to study the influence of fluorocarbon and hydrocarbon backbones on proton dissociation, the interaction of water molecules with the sulfonic acid group, and the energy barriers for proton dissociation. Better proton dissociation properties of CH3SO3H compared to CF3SO3H are observed from statistical analyses of the optimized structures for both systems. However, the calculated energy barriers for proton dissociation are lower for CF3SO3H than for the CH3SO3H system. At the same time, the interaction of water molecules is stronger for CH3SO3H than for CF3SO3H. Also, the analysis of the hydrogen-bonding network in both systems shows that the number of hydrogen bonds formed around the sulfonic acid group in CH3SO3H is larger than that in CF3SO3H. Therefore, the decrease of the energy barrier with increasing number of coordinating water molecules, pronounced in the case of CH3SO3H, may lower the barrier, which enhances good proton conductivity of a hydrocarbon-based polymer in low humidity conditions. Thus the hydration ability of a sulfonic acid group is an important factor for realizing better proton dissociation in low humidity conditions.