Under China’s railway-based coal transport system, railway-sea intermodal transport and land-sea complementary transport modes have gradually been developed. However, problems such as imperfect articulation mechanisms and poor information continue to affect the port’s operational efficiency. Through an in-depth analysis of the coordinated operation of trains and ships under the scenario of rail-sea intermodal transport, this study integrates key port operations such as unloading-coal distribution-loading with the goal of minimizing the cost of ship delays, establishing a mixed-integer planning model to study the co-optimization problem of train scheduling and ship coal distribution schemes in coal ports, and designing a heuristic method based on a variable neighborhood search to solve the model. Finally, this study uses a coal port in northern China as an example, conducting computational experiments using data of different sizes to verify the model’s effectiveness and provide management insights for future coal port operations.