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.