With the aggravation of global climate change and the proposal of the "dual-carbon" goal, it is urgent to optimize the organizational model of sea-rail intermodal transportation in Yangshan Port in order to improve the operational efficiency and achieve the green low-carbon development. Based on the analysis of the current situation and problems of the development of sea-rail intermodal transportation in Yangshan Port, the mechanism of the role of the underground logistics system in improving the level of sea-rail intermodal transportation in Yangshan Port is discussed， and an optimization strategy for sea-rail intermodal transportation in Yangshan Port based on the underground logistics system is put forward from the aspects of realizing the direct transportation in the port area, sharing the pressure of highway transportation, reducing the transportation costs and improving the reliability of intermodal transportation. The short-term scheme will strengthen the construction of underground freight channels in the Lingang Collection and Distribution Center and Luchaogang Container Central Station. The medium-term scheme will extend the channel to Situan Station in order to build an underground freight network covering the key logistics nodes. The long-term scheme will build a "Y"-shaped smart underground logistics network radiating the Yangtze River Delta region. Finally, the efficient, large-scale and automated operation of the port area is realized. At the same time, the price mechanism of sea-rail intermodal transportation can be improved by fully using the price advantage of underground logistics, and the flexible scheduling is adopted to improve the time reliability of sea-rail intermodal transportation in order to provide the decision-making references for the low-carbon transformation and sustainable development of the collection and distribution mode of Yangshan Port.