Aiming at the problem that the constant speed operation of the aquaculture water pump equipped by a large aquaculture worker ship will cause a lot of power waste and increase the aquaculture cost, a Whale Optimization Algorithm (WOA) Fuzzy PID controller for the aquaculture water pump is designed. The whale algorithm is used to optimize the quantitative factor and scaling factor in the Fuzzy PID controller, which makes the controller can dynamically adjust the speed of the aquaculture pump for the complex and changeable conditions of water changing, feeding, cleaning, and surface foam discharge, so as to realize the regulation of seawater flow. Simulation results show that compared with the PID controller and Fuzzy PID controller, the overshoot and steady-state error are smaller. The adjustment time is shortened by 71.11% compared with the PID controller and 44.29% compared with the Fuzzy PID controller, which can better meet the control requirements of the aquaculture water pump and achieve the goal of energy saving.