Abstract: The characteristics of heave compensation systems used on a marine drilling platform or on a drill-ship are analyzed. An active heave compensation system with two lift cylinders is proposed according to COMRA (China Ocean Mineral Resources & Association) pilot mining system for ocean poly-metallic nodule and the 1 000-meter-deep depth sea trial status. The corresponding virtual prototype is built. The parametric design, operation process and the performance of a fuzzy logic control on this virtual system have been simulated and investigated. The results show that this designed virtual system is feasible. The proposed fuzzy control policies can improve the effect of heave compensation, and reach the design target in virtual simulation.