The Mobile Harbor (MH) has been recently proposed as a novel maritime cargo transfer system that can move to a container ship anchored in the deep sea and handle containers directly at sea with the aid of a stabilized MH crane. Because this system operates under at-sea conditions, the MH crane must be designed to support an inertia load and wind force, as well as its self-weight. The wave-induced motions of the MH, e.g. rolling, pitching, and heaving, generate a significant amount of inertia load, which has not been considered in the design of conventional quayside cranes installed on stable ground. Wind force is also a critical design factor due to the higher wind velocity in the open sea. In addition to the aforementioned structural rigidity, mass minimization is also important in the structural design of MH cranes because it reduces the overturning moment and therefore enhances ship stability. In this paper, the sensitivities of the design-dependent loads (i.e. self-weight, inertia load, and wind force) are derived with respect to the design variables, and then a topology optimization is conducted with the derived sensitivities in order to obtain a conceptual design. Then, the conceptual design is elaborated into a three-dimensional basic design through shape optimization with design regulations for offshore cranes. Through the integrated design process with the topology and shape optimizations, a conceptual and basic design is successfully obtained for the MH crane.