To provide more rational design solutions at conceptual design level, axiomatic design method has been applied to solve critical part of a new engineering problem called Mobile Harbor. In the implementation, the Mobile Harbor, a functional harbor system that consists of a vessel with container crane approaches to a container ship anchored in the open sea and establishes a secure mooring between the two vessels to carry out loading and unloading of containers. For this moving harbor system to be able to operate successfully, a reliable and safe strategy to moor and maintain constant distance between the two vessels in winds and waves is required. The design process of automatic ship-to-ship mooring system to satisfy the requirements of establishing and maintaining secure mooring has been managed using axiomatic design principles. Properly defining and disseminating Functional Requirements, clarifying interface requirements between its subsystems, and identifying potential conflict, i.e. functional coupling, at the earliest stage of design as much as possible are all part of what need to be managed in a system design project. In this paper, we discuss the automatic docking system design project under the umbrella of KAIST mobile harbor project to illustrate how the Axiomatic Design process can facilitate design projects for a large and complex engineering system. The solidified design is presented as a result.