The invention discloses an active heave compensation system used in the process of deep-water lifting operation. The active heave compensation system comprises a motion calculation unit, a control unit, a hydraulic drive unit and a mechanical execution unit, wherein the motion calculation unit is used for detecting a heave motion signal of a working mother ship, a real-time speed signal of a suspended load and a real-time tension signal of a suspension cable, carrying out calculation based on a combination of the above detected signals and an input main control signal, and outputting a calculation result to the control unit; the control unit is used for calculating the signal to obtain an output signal to control the hydraulic drive unit; the hydraulic drive unit is connected with and arranged between the control unit and the mechanical execution unit for supplying power for the mechanical execution unit; and the mechanical execution unit is used for realizing non-linear heave motion for compensation of the suspension cable. The above-mentioned active heave compensation system provided by the invention can effectively control the vertical movement of the suspended load, reduces theinfluence of the vertical movement of the suspension cable on the whole construction process to the greatest extent, and improves safety, high efficiency and reliability of underwater construction, especially deep-water operation.