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As a comparative study, the global performance of two cases for a floating harbor system are researched by numerical analysis and compared with results from experiments: one is a two-body case such that a floating quay is placed next to a fixed quay, a normal harbor, and the other is a three-body case such that a container ship is posed in the middle of the floating quay and the fixed quay. The numerical modeling is built based on the experimental cases. Mooring system used in the experiments is simplified to sets of linear springs, and gaps between adjacent bodies are remarkably narrow as 1.3m~1.6m with reference to large scales of the floating structures; a water plane of the fixed quay is 480m×160m, and the ship is 15000 TEU (twenty-foot equivalent unit) class. With the experiment-based models, numerical analysis is implemented on two domains: frequency domain using a three dimensional constant panel method, WAMIT, and time domain using a coupled dynamic analysis program of moored floating structures, CHARM3D/HARP. Following general processes of the two main tools, additional two calibrations are implemented if necessary: revision of external stiffness and estimation of damping coefficients. The revision of the external stiffness is conducted to match natural frequency of the simulation with that of the experiment; to find out natural frequencies RAO comparison is used. The next, estimation of damping coefficients is carried out on time domain to match the responses of the simulation with those of the experiment. After optimization of the numerical analysis, a set of experimental results from regular wave tests is compared with RAO on frequency domain, and results from an irregular wave test of the experiment are compared with response histories of simulation on time domain. In addition, fender forces are compared between the simulation and experiment. Based on response histories relative motions of the floating quay and container ship are compared. And the floating harbor system, the three-body case, is compared with a conventional harbor system, a fixed quay on the portside of the container ship, in terms of motions of the container ship. As an additional simulation, the three-body case is investigated on an operating sea state condition. From the present research, the experimental results are well matched with the numerical results obtained from the simulation tools optimized to the experiments. In addition, the floating harbor system show more stable motions of the container ship than the conventional harbor system, and the floating harbor system in the operating sea state condition have motions even smaller enough to operate in term of relative motions between the floating quay and the container ship.