To solve the problem of water management subsystem fault diagnosis in a proton exchange membrane fuel cell (PEMFC) system, a novel approach based on learning vector quantization neural network (LVQNN) and kernel principal component analysis (KPCA) is proposed. In the proposed approach, the KPCA method is used for processing strongly coupled fault data with a high dimension to reduce the data dimension and to extract new low-dimensional fault feature data. The LVQNN method is used to carry out fault recognition using the fault feature data. The effectiveness of the proposed fault detection method is validated using the experimental data of the PEMFC power system. Results show that the proposed method can quickly and accurately diagnose the three health states: normal state, water flooding failure and membrane dry failure, and the recognition accuracy can reach 96.93%. Therefore, the method proposed in this paper is suitable for processing the fault data with a high dimension and abundant quantities, and provides a reference for the application of water management subsystem fault diagnosis of PEMFC.