Abstract: Fish have been an important human food source for a long time. In recent years, the development of high tech fisheries such as large-scale deep-water cages has led to a dramatic increase in the global supply from capture fisheries. However, traditional methods of fish transport by heavy lifting in a fish container are energy-intensive and result in great fish loss. Fish pumps have been developed as an efficient substitute for aquaculture to transfer the fish using less energy intensive systems and fewer losses that preserve the fish freshness. According to the operating principle, fish pumps can be classified as impeller fish pumps, pressure/vacuum fish pumps, and jet fish pumps. The impeller fish pumps have a special design to adapt to fish transport and the high-speed rotating impeller provides high transport capacity of fish but results in high fish mortality and injury rates. The water-ring vacuum-pump drives utilize vacuum and high-pressure regions which treat the fish more gently but lower capacities because of the discontinuous operations during suction and discharge stage. In the jet fish pump, the primary flow goes into a suction chamber via an annular nozzle and then creates a suction force on the secondary flow carrying the fish. The fish-water mixture then flows through the nozzle, throat and diffuser and is finally pumped out. Among these fish pumps, jet fish pump has the highest comprehensive properties giving consideration to transport capacity and mortality rate. Typical jet fish pump is composed by a suction duct, a primary duct, an annular nozzle, a suction chamber, a throat and a diffuser. The area ratio is the ratio of the throat sectional area to the annular nozzle sectional area and is a key parameter in a jet fish pump. In present paper, jet fish pumps with different area ratios (1.75 and 3) were designed and a series of experiment were conducted to study the transportation performance of jet fish pumps and relative injuries of Carassius auratus. The experiment results showed that the jet fish pump with smaller area ratio had a higher transportation capacity in the same secondary flow rate operation condition. The difference of transportation capacity caused by area ratio increased as the rise of secondary flow rate and the maximum transportation capacity difference reached 748 kg/h in the experiment. Moreover, the jet fish pump with smaller area ratio had lower energy consumption per unit mass in the same secondary flow rate operation condition. The difference of energy consumption per unit mass caused by area ratio increased as the rise of secondary flow rate and the maximum transportation capacity difference reached 1.31 kW?h/t. In the experiment, the external injuries of fish were classified as mild and severe injuries, and the main type external injury was mild injury. The severe injury rates caused by jet fish pumps with different area ratios showed no significant difference. Yet, the fish transported by the jet fish pump with smaller area ratio had a higher mild injury rate. The organs and serum of Carassius auratus were also checked. The transportation process of jet fish pumps affected the liver of fish and this influence was more significant when fish were transported by the jet fish pump with a bigger area ratio. The kidney of fish was also influenced but it could recover in 24 h after the transportation of jet fish pumps. Considering the transportation capacity and fish injury rates, the jet fish pump with smaller area ratio was more suitable for fish transportation. Consequently, the main contribution of our work is to demonstrate the influence of jet fish pump area ratio on the transportation performance and fish injuries caused. More importantly, the present paper provides guidelines for optimizing jet fish pumps considering transportation performance of jet fish pumps and injuries of fish.