A new concept of container transportation system called Mobile Harbor has been being developed recently in South Korea. The mobile harbor is a moving functional harbor which consists of a vessel with container crane and is capable of going out to a container ship for loading and unloading containers in open sea. For the Mobile Harbor to be able to operate in open seas, there should exist a reliable and safe strategy to maintain relatively constant distance between the Mobile Harbor and the container ship during the crane operation. To solve this problem, a novel ship-to-ship automatic mooring system that utilizes vacuum suction pads, robotic arms, winches, cables, and fenders has been developed. Furthermore, the developed system has been evaluated for its reliability and operational feasibility. Here, the details on the concept and operation strategy of the novel ship-to-ship automatic mooring system are introduced. In addition, explanations and discussions on various tests and operation experiments done for the system development are given.