The present disclosure relates to a system for fresh water supply using a desalination vessel and an autonomous navigation vessel, and more particularly, to a system for fresh water supply using a desalination vessel and an autonomous navigation vessel capable of, in providing fresh water to a plurality of islands using a vessel equipped with a desalination apparatus and an autonomous navigation vessel, setting an optimal fresh water supply route in consideration of the fresh water retention status of islands, location information of islands, and fresh water requirement amount for each route, and based on this, supplying fresh water to each of the islands, thereby minimizing the operation cost of the vessels and stably providing fresh water to the islands requiring fresh water, and the system for fresh water supply using a desalination vessel.