The running state of the hybrid tram and the service life of fuel cell stacks are related to the fault diagnosis strategy of the proton exchange membrane fuel cell (PEMFC) system. In order to accurately detect various fault types, a novel method is proposed to classify the different health states, which is composed of simulated annealing genetic algorithm fuzzy c-means clustering (SAGAFCM) and deep belief network (DBN) combined with synthetic minority over-sampling technique (SMOTE). Operation data generated by the tram are clustered by SAGAFCM algorithm, and valid data are selected as fault diagnosis samples which include the training sample and the test sample. However, the fault samples are usually unbalanced data. To reduce the influence of unbalanced data on the fault diagnosis accuracy, SMOTE is employed to form a new training sample by supplementing the data of the small sample. Then DBN is trained by the new training sample to obtain the fault diagnosis model. In this paper, the proposed method can well distinguish the four health states, which are high deionized water inlet temperature fault, hydrogen leakage fault, low air pressure fault and the normal state, with an accuracy of 99.97% for the training sample and 100% for the test sample. (C) 2020 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.