A dead-ended anode (DEA) has advantages such as simple structure, high reliability, and low price, and is widely utilized in polymer electrolyte membrane fuel cell (PEMFC) systems. Empirical parameters are commonly adopted in control-oriented models for such systems, and detailed information about mass transport processes is usually not available. Such models are neither helpful for understanding the internal processes within fuel cells, nor for designing control algorithms to improve system performance. A control-oriented model considering the mass transport processes and actuator properties is still lacking. This paper proposes a nonlinear dynamic mechanism model for the DEA system that can describe the dynamic voltage drop during water flooding with a large current density. The properties of the major components are explained in details, and the procedure of how the purging valves affects the mass transport and cell voltage is revealed quantitatively. The relationship between the minimum cell voltage and purging operations is summarized. The results show that (1) the proposed model can capture the stable and dynamic properties of a fuel cell with a DEA, (2) the cell voltage loss during closing of the purging valve is mainly caused by a decrease in oxygen and hydrogen partial pressures on the catalyst layers and an increase in the liquid water saturation ratio in the gas diffusion layers (GDLs); (3) the most important internal states that affect the stack voltage during purging is the liquid water saturation ratio in the GDLs.