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In this article, we propose a systematic approach to apply the simulation modeling and analysis for a flexible manufacturing system which includes a conveyor, AGVs(automated guided vehicle system) and AS/RS(automated storage and retrieval system). This paper presents the design(independent) parameters as objective function and critical(dependent) factors as constraints for the selection of design factors directly. Then the effective and fast solution procedure based on the pareto optimal solution set is proposed. This paper provides a comprehensive framework for the system design using the simulation and metamodels.