The article will first cluster the ports in the Yangtze River basin according to the water depth and throughput of the port area, analyze the adaptability of the ports in each cluster to the river-sea direct transport mode, and then select the cluster that is most suitable for the development of river-sea direct transport's port. In the case analysis, combine the three criteria of hub, channel conditions and loading and unloading capacity to carry out ANP network level analysis, and explore the factors that should be taken into consideration when the shipping company chooses a cooperative port. Finally, combined with the results obtained in the examples, it is suggested that the majority of shipping companies should consider the port's loading and unloading capacity and hub when seeking partners. Finally, suggestions are made on the cooperation methods between port companies and shipping companies, and new reference ideas are provided.