A two-dimensional multiphase proton exchange membrane fuel cell model is established to study the effect mechanism of temperature, pressure, humidity, and flow rate on the purge rate and ionomer dissolved water content at the end of purging on the basis of water heat transfer and water vapor phase change mechanism. The numerical model is analyzed by COMSOL Multiphysics 6.0 software, and the polarization curve and high-frequency impedance curve obtained under the same operating conditions are used to verify the validity of the model. Results show that ionomer dissolved water content increases and then decreases slightly due to the liquid water dissolved phase transfer in the slow-change step of the purge. Temperature, pressure, and humidity can effectively improve the purge rate and reduce the ionomer dissolved water content of the purge end. However, flow rate has little impact on both, but it can shorten the duration of the first stage and improve the effectiveness of the purge by effectively removing liquid water. This study provides a basis for revealing the influence of shutdown purge and formulating a reasonable shutdown purge strategy.