Cold start is one of the major issues that hinders the commercialization of polymer electrolyte membrane fuel cells (PEMFCs). In this study, a 2D transient multi-physics model is developed to simulate the cold start processes in a PEMFC. The phase change between water vapor, liquid water, and ice in the catalyst layers (CLs), micro porous layer (MPLs), and gas diffusion layers (GDLs) is also investigated, particularly the effect of ice crystallization kinetics when supercooled liquid water changes into ice. The factors affecting the different operating conditions and structural features of the membrane electrode assembly (MEA) are investigated. The results show that when the start temperature is −20 °C or higher, ice formation is delayed and the formation rate is decreased, and supercooled liquid water permeates from the CL into the MPL. For an MEA with relatively high hydrophobicity, the water permeation rate is high. These results can enable a PEMFC to start at subzero temperatures. The effect of ice crystallization kinetics is negligible when the fuel cell is started at −30 °C or below.