The axiomatic design principles are applied to the conceptual design of semi-submersible type mobile harbor (B1). The process of how the design of mobile harbor is elaborated, evaluated and improved from the very beginning is presented in this paper. The concept of mobile harbor is a functional harbor, which can move to a container ship anchoring out of ports in the deep water to load/unload containers on sea and transfer them to their destination ports. This floating system will innovate the maritime transport and distribution since it will greatly enhance the accessibility of super-sized container ships to existing harbors and harbors without enough infrastructures. Designing a mobile system which can perform the functions of traditional harbors on the floating system requires innovative ideas as well as rigorous validations of each sub systems. In order to enhance the chance of design success, we try to satisfy the design axioms in early stage of conceptual design. We use the zigzagging process for defining Functional Requirements (FR)-Design Parameters (DP) hierarchy due to the complexity of the system. In other words, we decomposed the complexity of the design by FR-DP hierarchy and reduced coupled design logically and systematically. This paper shows applicability of the axiomatic design principles to the field of ocean systems engineering.