A wave motion compensating platform has the function of compensating the ship’s generalized heave motion (a coupling result of roll, pitch and heave). It can decrease the impact of ship motion on some sea works and equipments. The hydraulic mechanism of platform system has the characteristics of nonlinear and big inertia. In order to compensate generalized heave motion effectively, an adaptive predictive control policy is used for controlling the hydraulic mechanism. Based on equal-dimension and new information, an automation regressive model can get adaptive multi-step prediction. The model parameter estimation based on the least square algorithm is easy to blow up and be unstable when the system has random noise. To improve the problem solution, a damped recursive least square algorithm is proposed to estimate the parameters on line. For the short regulation time, strong anti-disturbance ability and great robustness, a nonlinear PID controller whose gain parameters vary with errors is suitable for controlling the hydraulic mechanism. Using the collected experimental data, the simulations suggest that adopting the above adaptive predictive control policy to control hydraulic mechanism is able to decrease the generalized heave amplitude of wave motion compensating platform.