FMS reliability cannot be accurately evaluated without considering coupling relations between system elements. This paper presented a hierarchical and quantitative evaluation index system for FMS based on Petri net models and judgment matrix construction. In the proposed system, influencing factors and their coupling relations related to system elements including human, control systems and mechanical equipment, are analyzed. Based on the above analysis, FMS is described as a hierarchical system composed of the whole-level system, processing system and transfer system. Petri net for the running process of each system is modelled for reliability simulation analysis. And judgement matrices of indexes are constructed and combined with simulation of Petri net models to determine weighted values for influencing factors. Finally, an application example is completed to verify the effectiveness of the proposed system. Results indicate that the system can help to quantitatively evaluate the reliability of FMS based on availability indexes of elements, and clearly show weaknesses of the system from element level, which is a significant basis for the FMS reliability improvement during the design stage.