The fish pump is an important piece of power equipment for aquaculture, especially for deep-sea engineering vessels and cage culture. Fish pump research focuses on reducing fish body damage, improving survival rates, and increasing fish lifting efficiency. The research object in this paper is a new type of vacuum fish pump, with the aim of improving the hydraulic performance of the vacuum fish pump and reducing the damage to the fish body. The dependent variables include the dynamic change process of the flow state and flow field under diachronic conditions, the fluid simulation analysis of the vacuum pump body and the flow channel structure, the inlet flow rate of the fish pump, the negative pressure of the pipeline, and the impact force of the water flow on the inner wall of the tank. The independent variables include the operating conditions of the pump body and the fish pump. The Latin hypercube sampling method is used to extract 167 sets of calculation models for the independent variables, and multi-objective optimization is performed based on the NSGA-II algorithm for the hydrodynamic performance of the fish pump. On the basis of ensuring the fish body damage rate, the structural parameters of the vacuum fish pump with the optimal hydrodynamic performance under 167 sets of parameter values were obtained. The optimized parameters were then entered into the solver again, and the results showed that, in the optimal structural parameters under certain conditions, the direction of the incident water flow in the vacuum fish pump tank is close to the upper end of the tank body, which will reduce the speed of the fish-water mixed flow when entering the tank, thereby reducing the collision damage to the fish body. Currently, the water flow velocity at the water inlet is about 2.5 m/s, and the negative pressure value distribution gradient between the tank body and the water inlet pipeline is quite consistent, which can achieve good fish suction and fish lifting effects.