In order to quantify the failure performance of PEMFCs’ C/C composite bipolar plates (BPs) under considering the uncertainty in multiscale sizes and loads, the failure probability function (FPF) of BPs at cold start is estimated. A three-stage multiscale simulation method is proposed for mechanical behavior analysis of multi-component heterogeneous composites. And the efficient estimation of FPF for C/C composite BPs is achieved via the proposed multiscale simulation method and decoupling sparse integration method, in which the unified density weight is constructed to decouple the double-loop framework of analyzing FPF, thereby reducing the computational complexity. Results indicate that the dangerous positions of BPs are around the gas flow channels and bolt holes. And the dangerous components are the carbon matrix and the interface between the matrix and fiber. The radius of elliptical fibers affects the distribution of failure factors on microscopic components, thereby affecting the variation of failure probability with fiber sizes significantly. The distribution parameter of composite layer thickness in BPs has a significant effect on structural safety, and the FPF result can be used to effectively guide the design of structure. Therefore, the proposed method is of great significance for guiding the rapid parameter design of composite BPs.