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　judgment　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.