Ship transportation plays an increasingly important role in and accounts for a large proportion of cargo transport. Therefore, it is necessary to improve the quality of the trajectory control system of the ship for improving the transport efficiency and ensuring maritime safety. This paper deals with the advanced control system for the three-degrees-of-freedom model of the underactuated ship in the condition of uncertain disturbance. Based on the three-degrees-of-freedom model of the underactuated ship, the authors built a bilinear model of the ship by linearizing each nonlinear model section. Then, the authors used the state estimator to compensate for uncertain components and random disturbances in the model. Finally, the authors built the output-feedback predictive controller based on the channel-separation principle combined with direct observation of the continuous model for controlling the motion of the underactuated ship in the case of uncertain disturbance and the bound control signals. The result is that the movement quality of the underactuated ship is very good in the context of uncertain disturbance and bound control signals.