Aiming at the operating characteristics of the hydraulic lifting system of the jack-up wind turbine installation vessel with pin type, a two-stage hydraulic synchronous control system was designed. The mathematical modeling and analysis of the two-stage hydraulic synchronous control system were carried out, and the nonlinear mathematical model was established. The speed tracking-position coupling synchronization strategy and fuzzy PID algorithm were used for the single leg control; AMESim and Simulink were used for joint simulation, the synchronization performance under starting,eccentric load, proportional directional valve power failure and sensor interference was analyzed. The simulation results show that the two-stage hydraulic synchronous control system has the advantages of stable operation, no overshoot, high reliability, and high synchronization accuracy. The synchronous control system provides reference for the automation and intelligence of the jack-up wind turbine installation vessel’ s pile legs.