A tracking controller is proposed for a crane attached to a mobile harbor (MH) equipped with a dual-stage trolley system, to dynamically position a container from the MH to the container ship or vice versa. Wave-induced motions of the MH and container ship occur during loading and unloading operations owing to external disturbances such as waves. However, a challenging task is to move a payload with unwanted swing motions accurately to the loading and unloading positions on a moving target vessel. To solve this problem, a dynamic MH crane model is derived in three-dimensional space, with roll, pitch, and heave motions caused by sea-wave disturbances. The MH crane model is then linearized to design a tracking controller and the parameters of the linearized model are obtained by carrying out the system identification process. A preview tracking control method that includes feedback and feed-forward control with the predicted target position in the x-y plane in the near future is utilized. Through numerical simulations and experiments with a scaled model, the tracking performance of the proposed dynamic positioning control system is considered when sinusoidal roll and pitch motions of the MH are generated to mimic the wavy sea environment.