In order to solve the common problems of low fuel efficiency and insufficient fresh-keeping ability of motor fishing vessels in China, an aqueous-ammonia absorption refrigeration system driven by recovering waste heat from the exhaust gas of diesel engines was introduced. Based on Aspen Plus, the refrigeration cycle model was built, and the refrigeration cycle processes with a cooling capacity of 15 kW, 20 kW and 25 kW were simulated. It was found that when the target cooling capacity is 20 kW and 25 kW, and the refrigerant flow increases to a certain range, the heat load of the generator appears straight, which illustrates that the heat provided by exhaust gas can’t make the refrigerant separate out enough pure ammonia to satisfy refrigeration requirements. At the same time, the “low-lying” period appears in the curve of the coefficient of performance, and for the whole refrigeration system, its economic and heat efficiency is at unfavorable level. Therefore such conditions should be avoided in actual operations. In the cycles with the target cooling capacity of 15 and 25 kW, the coefficient of performance and actual cooling capacity increases sharply when the gas flow is huge, which is harmful for the reliability and economy of the system, thus the gas flow should be properly controlled in actual operations.