Compared with the open space of the aquaculture cage, the space of the aquaculture ship is closed and narrow, which is difficult to accommodate the huge suction pump operation equipment. At present, the centrifugal suction pump has the advantages of compact structure, flexible installation and not out of water during the whole fishing process compared with the vacuum type and jet flow, which is especially suitable for the aquaculture ship. To address the challenge of minimizing fish damage and enhancing the efficiency of fish collection in aquaculture ship, a low-damage fish suction pump with a diameter of 200 mm has been developed. The computational fluid dynamics-discrete element method (CFD-DEM) is used to analyze the flow field characteristics of the impeller and optimize the performance of the suction pump. Flow line distribution is uniform, no fish body extrusion and blockage; at the same time, the pressure distribution in the pump channel is uniform, and it will not cause too much damage to the fish. Fish suction pump test, at the outlet end with a net bag to separate the fish water, the results show that only a small number of shark sucker has slight scratches, suspected to be scratched by a mesh bag during the separation, and no trace of impeller scratches, meet the non-destructive live fish transport requirements. The results show demonstrates that fish suction pumps can be adapted to accommodate various fish species by adjusting the pump's diameter and rotational speed. This customization minimizes fish injury, reduces the physical labor required, and enhances both the efficiency of fish harvesting and the survival rate of the caught fish.