In proton exchange membrane fuel cells (PEMFCs), free radicals easily attack ionomers, resulting in membrane degradation. In this work, the multistate empirical valence bond (MS-EVB) method is employed to investigate the chemical degradation impact of Nafion membranes on proton transport and the solvation effect. The hydrophilic domain and its connectivity are analyzed. The numbers of surrounding water and hydronium ions as well as the location of the solvation shell are evaluated. The results demonstrate that the membrane degradation does not change the interaction with the hydronium ions and water molecules but alters the coordination number, leading to a larger hydrophilic domain and a poorer connectivity. The acid groups and protons are distributed more at the edge of the hydrophilic region to accelerate the proton motion, which is not conducive to the proton transport along the membrane side chain.