The proton exchange membrane fuel cell (PEMFC) best exploitation needs to be based on reliability and fault tolerant control. One of the issues to fulfill this objective is ensuring high reliability indexes of the associated DC/DC converter, which is indispensable in practice. Three-stage interleaved boost converter is proposed in this context with a reliability-based reconfiguration control. The proposed control approach is passivity based, it is robust against high-temperature variations and load perturbations. However, this article proposes a novel method that adapts the reference current by a linear transformation. The fault tolerant control manages the open circuit failure to adapt the control algorithm to two-stage converter reconfigured structure. The matlab/simulink-based simulations show the effectiveness of the proposed control scheme as well as the reconfiguration method, which can give a technical improvement in the exploitation of PEMFC power supplies in the presence of faults and perturbations.