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Based on the seaworthiness characteristics of the waterways and the container origin-destination (OD) flows between the riverside ports on the Yangtze River, China, this article aims to build an integer programming model to optimize the container liner network on the Yangtze River by minimizing the total transportation cost. The model can determine the shipping routes, calling ports, calling sequences, number and type of the used ships. In order to make the model usable, we formulate the waterway’s impedance function and designs a genetic algorithm (GA) based on Frank–Wolf method. In the optimized network, the big ships are used in the midstream of the River while the small ones are adopted on both ends. It differs from the current ship allocating principle by which the small ones run in the upstream while the big ones run in other segments. [ABSTRACT FROM AUTHOR]