To study the accurate calculation and fault mode diagnosis of supply chain, a new method-GO methodology is applied in reliability analysis of supply chain. Through analyzing every important factor leading to success of supply chain system and taking three-tier supply chain as the object, GO model of reliability analysis of supply chain is developed. The model can not only calculate reliability of supply chain system in detail, but also diagnose its failure mode and calculate its importance, which provides the way for improving and optimizing supply chain system. The example is presented to prove the method’s feasibility and validity.