A new concept sea-floating port called mobile harbor has been introduced, in order to resolve the limitation of current above-ground port facilities against the continuous growth of worldwide marine transportation. One of important subjects in the design of a mobile harbor is to secure the dynamic stability against wave-induced excitation, because a relatively large-scale heavy crane system installed at the top of mobile harbor should load/unload containers at sea under the sea state up to level 3. In this context, this paper addresses a two-step sequential analytical-numerical method for analyzing the structural dynamic response of the mobile harbor crane system to the wave-induced rolling excitation. The rigid ship motion of mobile harbor by wave is analytically solved, and the flexible dynamic response of the crane system by the rigid ship motion is analyzed by the finite element method. The hydrodynamic effect between sea water and mobile harbor is reflected by means of the added moment of inertia.