Trawlers tend to be subjected to wind and wave movements, which in turn affects fishing efficiency and safety. In order to eliminate the influence of the heave motion of trawlers, an automatic adjustment device of hydraulic cylinder heave compensator based on Fuzzy PID controller is designed in this paper. Firstly, the principle of active hydraulic cylinder heave compensation scheme is analyzed. Taking the valve controlled asymmetric cylinder position control system as the research object, the mathematical model is established, the fuzzy PID controller is designed. The fuzzy PID and classical PID simulation models are built in Matlab/Simulink, and the heave compensation performance of the system is simulated in different sea conditions. The results show that under the fuzzy PID control, the overshoot of the system is reduced by 0.06 m and the adjustment time is shortened by 0.11 s compared with the classical PID control, and the system has low position tracking error and good anti-interference ability. The heave compensator can better adapt to different sea conditions under Fuzzy PID control. This study will provide a reference for the study of heave compensation of trawlers.