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Based on the idea that modules are independent of machines, different combinations of modules and machines result in different configurations and the system performances differ under different configurations, a kind of cyclic reconfigurable flow shops are proposed for the new manufacturing paradigm-reconfigurable manufacturing system. The cyclic reconfigurable flow shop is modeled as a timed event graph. The optimal configuration is defined as the one under which the cyclic reconfigurable flow shop functions with the minimum cycle time and the minimum number of pallets. The optimal configuration, the minimum cycle time and the minimum number of pallets can be obtained in two steps.