Abstract: Abstract: Low-carbon refrigeration is a promising trend in cold chain logistics under carbon peaking and carbon neutrality. Among them, CO2 refrigeration has offered broad application prospects in freezing and cold storage of agricultural products. In addition, the different agricultural products vary greatly in the temperature requirement of the storage. The single temperature zone in the current storage systems cannot fully meet the high-quality storage in the various agricultural products. Fortunately, the cascade refrigeration system can be expected to utilize in cold storage, due to the wide temperature range and high performance. Different temperature zones can be set in the high and low-temperature cycle of the cascade refrigeration system, in order to achieve accurate temperature control of materials, according to the storage characteristics of different agricultural products. In this study, the double- and three-temperature zones were applied to the cascade refrigeration system in cold storage. The natural CO2 was selected as the refrigerant in the low-temperature cycle, while the potential environment-friendly fluid R513A was used in the high-temperature cycle of the systems. The pressure difference was reduced in the different temperature zones, where a booster compressor (booster system for short) was set behind the evaporator with the low evaporation temperature, and a pressure regulating valve (throttling system for short) behind the evaporator with the high evaporation temperature. Furthermore, a thermodynamic model was established for the double- and three-temperature zone cascade refrigeration system, and then to carry out the energy and exergy analysis. A systematic investigation was made to clarify the effects of condensation temperature in the low and high-temperature cycle, temperature difference of cascade heat transfer on the coefficient of performance (COP) and exergy efficiency (ηe) of cascade refrigeration systems. The COP and exergy efficiency of the multi-temperature zone refrigeration system decreased both in the booster and throttling mode, particularly with the increase of the condensation temperature in the high-temperature cycle and the temperature difference of the cascade heat exchanger. The performance of the double-temperature zone cascade refrigeration and the booster system of the three-temperature zone cascade refrigeration cycle increased firstly and then decreased with the increase of the condensation temperature in the low-temperature cycle. The performance of the throttling system increased gradually for three temperature zone. The results also showed that the coefficient of performance and exergy efficiency of the booster system was higher than those of the throttling system, at the reference working conditions, the coefficient of performance of double temperature zone and three temperature zone booster system was increased by 30.4% and 23.4% respectively. The exergy destruction analysis found that the condenser had the largest exergy destruction, and the exergy destruction of the pressure regulating valve was much higher than that of the booster compressor. Under the same operating conditions, coefficients of performance of the double and three temperature zone booster systems designed in this study institute are 1.5 and 2.3 times that of the CO2/R134a single temperature zone cascade system. A higher performance was achieved in the multi-temperature cascade refrigeration system. The initial investment and maintenance cost, system operation cost, and environmental cost were lower in the double temperature zone cascade refrigeration cycle booster system, compared with the throttling system. The total annual cost of the system was still far less than that of the throttling system, even the initial investment and maintenance cost was higher in the three-temperature zone cascade refrigeration cycle booster system. Although the initial investment and maintenance cost of the three temperature zone cascade refrigeration cycle booster system was higher, the annual total cost of the double- and three-temperature zone cascade refrigeration cycle throttling system was USD 6554 and USD 8156 higher than that of the booster system, respectively. The total annual cost of the booster system was lower than that of the throttling system, due to the performance advantages.Therefore, the multi-temperature zone booster system was superior to the throttling system in terms of thermal performance and economy.