To address the issue of trajectory tracking under dynamic wave disturbances, this study proposes a nonlinear model predictive control method based on disturbance observer (DO-NMPC). The disturbance observer performs online observation of the generalized disturbance forces encountered by the unmanned platform during its motion, estimating the loads caused by wave disturbances in real-time. This information is used for active compensation in the model predictive control algorithm, enabling the control system to actively suppress wave disturbances related to unmodeled dynamics that cannot be measured. Simulation tests were conducted to compare the performance of the proposed DO-NMPC control strategy with the LQR control strategy in tracking straight-line and rotational trajectories on the water surface under wave disturbances. The simulation results validate the robustness and advantages of the proposed control strategy.