In the operation of proton exchange membrane fuel cells (PEMFCs), the ionomer-perfluorosulfonic acid (PSFA) membrane side chains are easily attacked by free radicals, resulting in membrane degradation. In this work, the chemical degradation effect of side chains in the PSFA membrane on proton dissociation and transfer behaviors is investigated by means of the quantum chemistry calculation. The rotation of the H atom in the acid group after the degradation is evaluated. The impact of the electrostatic potential (ESP) and electronegativity of the side chains is analyzed. The results demonstrate that the membrane degradation decreases the positive potential of the proton in the acid group, leading to the proton being less active so that more water molecules are required for the spontaneous proton dissociation. The rotation of the H atom in the acid group affects the proton dissociation mode owing to the change of the hydrogen bond network. It is found that the ESP of the acid group in two side chain fragments influences each other and the water molecules between two side chains can be shared to reduce the number of water molecules for the proton dissociation.