Abstract: Proton exchange membrane fuel cell (PEMFC), as an efficient and eco-friendly energy conversion device, has a broaden prospect on industrial application. However, the characteristics of multi-auxiliary systems and the multiphysics coupling phenomenon during operation make water management issues, thermal management failure, and reactant starvation and so forth easy to occur as well as hard to control in PEMFC. To eliminate the faults effectively and in time while maintaining the performance and improving the durability, the fault tolerant control (FTC) methodology with the superiorities of real-time and online characteristics, and high-diagnostic accuracy, is employed to optimize PEMFC operation. The FTC methodology can be divided into two parts of fault diagnosis and control redesign. Model-based and non-model-based fault diagnosis methods were reviewed in this paper, their merits and demerits were concluded as well, respectively. The function and necessity of the controller-regulating module and the decision-making module were introduced in the form of structure diagram. The existing studies of the FTC applied to PEMFC systems were reviewed as well. Finally, in the PEMFC field, the improvements needed for the existing studies and the prospects of the FTC were summarized.