The reliability and durability of the proton exchange membrane (PEM) fuel cells are vital factors restricting their applications. Therefore, establishing an online fault diagnosis system is of great significance. In this paper, a multi-stage fault diagnosis method for the PEM fuel cell is proposed. First, the tests of electrochemical impedance spectroscopy under various fault conditions are conducted. Specifically, prone recoverable faults, such as flooding, membrane drying, and air starvation, are included, and different fault degrees from minor, moderate to severe, are covered. Based on this, an equivalent circuit model (ECM) is selected to fit impedance spectroscopy by the hybrid genetic particle swarm optimization algorithm, and then fault features are determined by the analysis of each model parameter under different fault conditions. Furthermore, a multi-stage fault diagnosis model is constructed with the support vector machine with the binary tree, in which fault features obtained from the ECM are used as the characteristic inputs to realize the fault classification (including fault type and fault degree) online. The results show that the accuracy of the basic fault test and subdivided fault test can reach 100% and 98.3%, respectively, which indicates that the proposed diagnosis method can effectively identify flooding, drying, and air starvation of PEM fuel cells.