In this study, a motion control problem for the vessels towed by tugboats or towing ships on the sea is considered. The towed vessels, such as barge ships, are used for several purposes. Generally, these vessels have no power propulsion system and are towed using ropes and towing vessel (tugboats). The basic mathematical model of the towed vessel in which three active rudders are attached was introduced from a previous study. Owing to the dependency of the motions of the towed vessel to the towing ship, a method is suggested to cope with the undesirable disturbance and improve the tracking performance. For the simulation study, a model of the towed vessel with a towing ship is made, and necessary physical parameters are identified from the experiment. For the defined and linearized model, a control system is designed, and the control performance is also evaluated. A simulation study is conducted and the effectiveness of the proposed control strategy is verified