The parameter estimation of a molten carbonate fuel cell (MCFC) model is presented. The model is dynamic, spatially distributed, and describes a cross-flow configuration of the gas channels. It includes direct and indirect internal reforming, a catalytic combustor, and a reversal chamber between the anode and the cathode. The parameter estimation is based on measurements at a full-scale industrial MCFC plant. Because of the complexity of the model, the high number of parameters, and limited measurements, a specific strategy for the parameter adjustment has been developed. It includes a system balancing, sensitivity analysis and stepwise optimization of single parameters and parameter groups.