In this study, a more accurate model of a fuel cell of molten carbonate was also used to determine input and output control variables and to investigate the behavior of the system with respect to those variables. A more complete kinetic was also implemented to increase the effectiveness of the presented paper. The input variables, methane andcell voltage, are included in the fuel flow rate of cell. The output of the model is the flow resulting from the cell which is a function of the electrochemical reaction rate, and accordingly also a function of the state variables quantities. In the following, the model was used to simulate step response of each input and then the Dynamic behavior of cell was analyzed. The results indicate that as the fuel flow rate into the celllessens, the productivity of the fuel gets higher. Also, in the analysis of the fuel cell it was seen that the temperature of molten carbonate depends strongly on the amount of combustion of compositions in the combustion chamber. As the inlet concentration of methane, hydrogen and carbon monoxide increased, the heat liberated from combustion was more and increasing the system temperature which results in increased thermal stress in the molten carbonate fuel cell.