The invention designs a sea wave active compensation system of a hybrid mechanism. The sea wave active compensation system of the hybrid mechanism can detect a posture and a displacement of a maintenance ship after the maintenance ship is affected by sea waves, and active compensation of the sea waves can be achieved by controlling the hybrid mechanism. The sea wave active compensation system of the hybrid mechanism includes a hybrid mechanism, a detection system, a motion control system and an electric system; the hybrid mechanism includes an upper platform and a six-freedom degree parallel platform, and is an execution mechanism of the sea wave active compensation system, and an execution element adopts a hydraulic cylinder and a hydraulic motor; the detection system is used for detecting a position and a posture change parameter of the ship and a state parameter of the hybrid mechanism, and providing control information feedback for the control system; the motion control system canprovide real-time control quantity for the hybrid mechanism according to the parameters detected by the detection system through model calculation and motion control computing; and the electric systemcan provide a stable energy electric power for the whole mechanism, and can achieve man-machine information connection and system parameter real-time monitoring and so on.