Waste heat recovery of the fuel cell stack cooling system is very important from the viewpoint of effective use of energy. Simultaneously, temperature control of the fuel cell stack is necessary to maintain high electrical efficiency and to prevent the cell stack from oxidation. In phosphoric acid fuel cell system, coolant temperature is controlled to keep constant the temperature of cell stack. The purpose of this paper is to propose the simple dynamic model for designing the temperature control system and heat recovery system of fuel cell stack cooling system. In addtion to this, experimental research and simulation analysis reveal the dynamic characteristics of fuel cell stack cooling system with control equipments. Throughout the researches, concentrated parameter dynamic model is proposed and the validity of the model is confirmed by experimental results. When the transient response to disturbances such as make-up water pump start up is calculated, it is clarified that the coolant temperature of fuel cell stack can be controlled.