Fuel cell shutdown purge is an important method to improve the success rate of cold start. In this paper, a two-dimensional transient proton exchange membrane fuel cell (PEMFC) model is established to study the shutdown purge process of PEMFC under the hydrogen air purge strategy. Based on the GDL real pore model, PEMFC related conservation equation and ionomer gas phase transfer equation, the influence of the different humidity of purge gases on the purge speed and the membrane-bound water content after the purge, and the influence of the real pore structure of GDL on the internal mass transfer phenomenon of GDL during the shutdown purge stage were studied. The results show that the decrease in humidity of purge gas can effectively promote the gas phase transfer of membrane-bound water during the shutdown blowing process, thereby reducing the final water content; the real pore structure can provide a more realistic explanation of the transfer rule of water and gas during purge.