Abstract: The waterway transportation system is a mode of transportation that takes ships as the means of transport, ports as nodes, and oceans, rivers, lakes and other waters as channels, which can realize the carrying and space-time displacement of goods and personnel, and is an indispensable and important part of the comprehensive transportation system. This paper analyzes current development of waterway transportation systems, sorts out the future requirement and technical characteristics of waterway transportation systems, and puts forward the future development directions of waterway transportation systems, such as waterway transportation planning and organizational optimization, energy-efficient ship propulsive system and supply system, human-machine integrated ship shore-based driving control system, sea area multidimensional integrated transportation system, waterway transportation control system, meteorological navigation and safe navigation, etc., so as to provide theoretical basis and technical support for improving the operational efficiency and service quality of waterway transportation system.