The application of proton-exchange membrane fuel cells (PEMFCs) in maritime transportation is currently in the spotlight due to stringent emissions regulations and the establishment of a carbon trading system. However, salt in the marine environment can accelerate the degradation of proton-exchange membranes (PEM), which are the core component of PEMFCs. In this study, the effect of the NaCl concentration and temperature on the degradation of Nafion, the benchmark PEMFC membrane, was analyzed ex situ by accelerated degradation using Fenton’s test. The membrane properties were studied by mass change, fluoride ion emission, FTIR spectroscopy, and tensile test. The results showed that the degradation of Nafion membranes increased with the increase in temperature and NaCl concentration. Further studies revealed that Nafion produces C=O bonds during the degradation process. Additionally, it was found that sodium ions replace hydrogen ions in degraded Nafion fragments based on analysis of the weight change, and the rate of substitution increases with increasing temperature. A better understanding of the degradation behavior of Nafion in salty environments will lead to the advanced manufacturing of PEM for applications of PEMFCs in maritime transportation.