The hydraulic lifting type deep-sea multi-metal manganese nodules mining technology is widely used in deep-sea mining as a cutting-edge technology. In the mining process, due to the influence of ocean wind, waves, current and tide, the mining ship is inevitably in the direction of gravity. A significant heave movement occurs on the top. In order to improve the stability, reliability and service life of the mining pipe and the working efficiency and economy of the entire mining system. A set of lift pipe compensation system should be installed between the upper part of the pipe and the mining ship. Based on the above background, the purpose of this paper is to study the application of fuzzy control in the deep sea mining pipe heave compensation system. In this paper, the idea of fuzzy control is proposed for the time-varying, nonlinear and mathematical models of hydraulic system. The system adopts three main control strategies, namely fuzzy control, fuzzy self-tuning PID control and fuzzy PID composite control. The results show that the classical PID control displacement is between -4.5 and 4.5 mm, while the fuzzy self-tuning PID control displacement is between -4.2 and 2.2 mm, which improves the accuracy of PID control. It can be seen in the fuzzy control with different discrete levels that the large discrete level fuzzy control is obviously higher than the precision of the small discrete level control. It can reach -1.7 to 0.5 mm, greatly improving its accuracy. They are both robust to classical PID control and show good results in control. Among them, fuzzy PID composite control is more superior and practical.