A hybrid automaton modeling approach that incorporates state space partitioning, phase dynamic modeling and control law synthesis by control strategy is utilized to develop a hybrid automaton model of molten carbonate fuel cell (MCFC) stack shutdown. The shutdown operation is divided into several phases and their boundaries are decided according to a control strategy, which is a set of specifications about the dynamics of MCFC stack during shutdown. According to the control strategy, the specification of increasing stack temperature is satisfied in a phase that can be modeled accurately. The model for phase that has complex dynamic is approximated. The duration of this kind of phase is decreased to minimize the error caused by model approximation.