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An effective online fault diagnosis system is of great significance to improve the reliability of fuel cell vehicles. In this paper, a fault diagnosis model for proton exchange membrane fuel cells is proposed. Firstly, the tests of electrochemical impedance spectroscopy under different fault types (flooding, drying, air starvation) and fault degrees (minor, moderate, severe) are carried out, and each polarization loss of the fuel cell is denoted by an equivalent circuit model (ECM). Then, the parameters of the ECM are identified by the proposed random mutation differential evolution algorithm. Furthermore, the parameters identified under different fault conditions are used to train and test a probabilistic neural network-based fault diagnosis model. The fault diagnosis model achieves diagnosis accuracies of 100% for the fault type and 96.67% for the fault degree. By setting operating conditions with different fault degrees, the fault diagnosis model proposed in this paper can realize the fault type and fault degree diagnosis, effectively avoiding the misjudgment of fault types, and is effective for improving the reliability of the fuel cell system.