Reconfigurable Manufacturing Systems (RMSs) are widely used to produce small batches of customized products in the current manufacturing environment. We comprehensively optimized the assembly transport strategy, production process, and production configuration of a reconfigurable flow shop (RFS). Firstly, three assembly transfer strategies, one-to-one, one-to-many, and many-to-many, are proposed for an RFS, given the specific process limitations. In addition, a production simulation model of the RFS is established by the Plant Simulation software to verify and compare those three strategies with realistic production constraints considered. Moreover, the production processes are optimized, and the optimal buffer configuration and vehicle configuration are optimized by the design of experiment (DOE) method. After the optimization processes, the throughput and facility utilization under each strategy increases significantly. Additionally, the optimal buffer size and vehicle quantity under each strategy are determined and compared. The one-toone strategy can maximize the production output, but it requires the most production resources. In addition, the many-to-many strategy is more efficient than the one-to-many strategy. Our study provides a variety of assembly transport strategies for an RFS and offers an efficient optimization method for production performance and production configuration. (C) 2020 CPE, University of Maribor. All rights reserved.