The intricate structure of port-centric supply chain together with various uncertainties and participants existed make its scheduling issue complicated. To achieve an effective and cost-saving management, and meet the challenge of developing sustainable supply chain, this paper proposes a practical integrated scheduling model to minimize the over-all cost including production cost, storage cost, transportation cost, and final delivery penalty for a typical port-centric supply chain considering seaborne uncertainties. Specifically, not only a ship’s uncertain arrival time, but also its uncertain departure time caused by variable draft requirements and tidal level are considered. Then, a multilevel coding genetic algorithm with reduced feasible region is developed to solve this bi-level decision-making problem. The results of a case study show that the integrated scheduling method proposed in this paper can save 13% of total cost compared to first-come/first-served scheduling and give a clear grasp on resource bottleneck in port-centric supply chain. Moreover, the green policy-“Take the Tide” permission-in the origin port can increase the practical draft depth and cut down the overall cost, but will bring more challenges in inventory management, especially for the destination port.