A scheme is obtained by using some kinds of Petri net refinement, according to the design of flexible manufacturing system. Two kinds of refinement are obtained. Dynamic properties have been investigated. The sufficient and necessary conditions of liveness preservation, boundedness preservation and reversibility preservation are presented. A flexible manufacturing system has been designed and verified. These results are useful for studying the static and dynamic properties of Petri nets and analyzing properties of large complex system. The refinement method is especially fit for the design of flexible manufacturing system and practical to use in reality.