In this paper, the performance characteristics of a cryogenic refrigeration system used in fields such as HMR(Home Meal Replacement) that require ultra-low temperatures of -50℃ using natural refrigerants according to the recent enforcement of the Atmosphere Environment Conservation Act were investigated. For this purpose, a 2-stage compression refrigeration system using R744(CO2) and a cascade refrigeration system using R747/R404A and R747/R717(NH3) were applied. The COP(coefficients of performance) of each refrigeration system were compared according to changes in evaporation and condensation temperature, subcooled and superheated degree. Although the coefficient of performance of the 2-stage compression refrigeration system using R744 was superior to that of the cascade refrigeration system, 2-stage refrigeration system was considered that various problems should be solved in practical terms. In addition, the COP of R744/R717 for various operating conditions showed similar results to R744/R404A, so the possibility of alternativeness could be confirmed in the cascade refrigeration system.