Ship-borne manipulator system is extremely unstable under the complex marine environment, which seriously threatens the safety of operating equipment and operators. In this paper, the dynamics and robust control of wave compensation system for ship-borne manipulator are studied. First, based on the oil circuit variable amplitude control of ship-borne manipulator, the coupling dynamic model of valve-controlled cylinder parallel accumulator is established. Then, since traditional sliding mode needs high-order derivative of feedback angle, it is difficult to implement traditional sliding mode in real hardware system. To solve these problems, a nonlinear differential and integral sliding mode control strategy is proposed. The integral term is introduced to reduce the influence of unmodeled disturbance and parameter perturbation. The stability analysis proves that the system state can track the desired target signal, and the tracking error e( t) tends to zero. In addition, in order to weaken the phenomenon of system chattering, this paper introduces a nonlinear differential control to increase the damping coefficient of the system. The simulation and experimental results show that the control law has good dynamic performance, high control accuracy, and strong anti-disturbance ability without chattering phenomenon. It is of great significance to improve the efficiency and safety of ship-borne manipulator operation, and this paper also provides useful reference for wave compensation system of other marine equipment.