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This paper studies a practical multi-factory job allocation and scheduling problem involving inland and maritime transport limits. A new heuristic called Due-date Based Cut-off rule (DBC) is developed to improve the computational efficiency of both exact and genetic algorithms (GA). Except the application of DBC, this proposed GA is guided by a novel fuzzy controller aimed at eliminating the drawbacks other GAs have when dealing with multi-factory models. The tests of the solution quality and computational efficiency for this GA are carried out. The numerical experiments demonstrate the value of the proposed approach in this practical global supply chain.