The safety of personnel and cargo transfer tasks at sea is significantly affected by the vessel motion caused by waves. The conventional ship-mounted stabilization platform based on the Stewart–Gough platform has limitations such as a small vertical workspace and actuation parts installed on the moving links. To better meet the requirements of heavy-duty ship-mounted stabilization tasks, this study proposes a novel 6-PUS parallel stabilization platform. The kinematic model, including ship motion, is established in a non-inertial frame, and the dynamic model accounts for the mass and inertia characteristics of the limbs is derived. To address the control challenges caused by various internal and external disturbances at sea, this paper combines inverse dynamic control with the equivalent input disturbance approach. Disturbance effects are counteracted by establishing a disturbance estimation term and applying an opposite control signal to the input channel. Simulation results show that the proposed scheme has superior resistance to internal and external disturbances compared to conventional inverse kinematic or dynamic control, which significantly improved trajectory tracking performance in motion compensation tasks.