The present application discloses is a scheduling method and system for fully autonomous waterborne inter terminal transportation, and belongs to the field of transportation. The method includes: establishing a dynamic scheduling model for waterborne Autonomous guided vessels (wAGVs); quickly inserting the dynamically arriving transportation tasks into all the existing wAGV paths, calculating the insertion cost and selecting the path and position with the lowest insertion cost to obtain updated initial paths; improving the initial path using a heuristic algorithm based on tabu search to obtain quasi-optimal wAGV paths; executing the scheduling wAGV paths. The scheduling model of the present application is based on the combinatorial optimization, and considers performance indexes such as transportation distance and customer satisfaction, and constraints such as time window and loading capacity. An initial path by using an insertion method within the framework of rolling horizon is constructed. The initial path is then optimized and improved by designing a tabu search heuristic so that obtaining quasi-optimal multi-wAGV paths are obtained in real time. This system is helpful to improve the autonomy level of large ports.