A hybrid fuzzy P+ID controller is proposed and applied to the heave compensation system using an electro-hydraulic winch system. The heave compensation system can decouple the operation of underwater vehicle from the motion of vessel. Firstly, the heave motion of vessel is calculated based on measurements from an inertial measurement unit (IMU) using a digital high-pass filter. Then, a mathematical model of the electro-hydraulic winch system is developed, and the heave compensation controller based on hybrid fuzzy P+ID controller is designed to control the winch rotation according to the vessel motion. Finally, simulation studies and real device experiments are conducted to demonstrate that the heave compensation systems based on the fuzzy P+ID controller is much more robust than the conventional PID controller.