In recent years, with the steady development of China's economy, China's comprehensive transportation system has become increasingly perfect. In particular, the implementation of the " One Belt, One Road" strategy and the "Thirteenth Five-Year Plan" Comprehensive Transportation System Planning has provided a lot of convenience for the development of China's sea-rail combined transportation. However, judging from the current development of container sea-rail intermodal transportation in my country, the proportion of sea-rail intermodal transportation in port collection and distribution is low, and the connection between railway and waterway is not smooth, and sea-rail intermodal transportation needs to be developed urgently. Among the many factors restricting the development of my country's container sea-rail intermodal transport, the flow of containers to the port is a very important factor. Due to the uncertainty of the flow of containers arriving at the port, the sea-rail intermodal containers are not connected smoothly in the port, so that the staying time in the port is too long, which also affects the reliability of the container train transportation organization. This paper mainly takes the sea-rail intermodal transport container train as the research object, considering the uncertainty of the port container flow, studies the transportation organization of the train under the background of the Belt and Road, improves the operation efficiency of the train, and promotes the development of the sea-rail intermodal transport in China.