Under the background of the “Belt and Road” Initiative, the Lancang-Mekong Cooperation Mechanism takes “connectivity” as one of the five priority cooperation directions, and new requirements have been put forward for shipping governance in the basin. With the development of globalization, informatization and regional integration, the traditional mode of single bureaucracy governance and market governance in the basin frequently fails, and the network governance provides different perspectives and methods. A multi-level network governance structure with dual structural characteristics of “circle” and “network” makes joint efforts through the governance methods of bureaucracy, market and network from the three levels of government, market and society. The lessons from the successful governance experience of the Rhine river and the Nile are drawn, and more governance powers are given to the water-related enterprises, people, NGOs, think tanks, media and research institutions. Eventually, based on the actual situation, a multi-level network governance mechanism is proposed to improve the plight of cross-border shipping cooperation in Lancang-Mekong River basin.