This paper examines the exergy efficiency and exergy destruction rate of the R744/R404A cascade refrigeration system (CRS) using an internal heat exchanger in supermarkets according to various conditions affecting the system. A refrigerant of a low-temperature cycle uses R744 and a refrigerant of a high-temperature cycle in the CRS uses R404A. Experiments were conducted by changing various conditions on the high- and low-temperature side, and exergy analysis was performed accordingly. The main results are summarized as follows: (1) the lower the total exergy destruction rate of the CRS, the higher the exergy efficiency of the system, and accordingly the coefficient of performance (COP) of the system is also improved. (2) In the CRS, since the optimum cascade evaporation temperature exists (about −16 °C), it can be said that the limit point, that is, the cascade evaporation temperature with the maximum COP of the system, is the optimum point at about −16 °C. Therefore, at this optimum point, the exergy destruction rate of the cascade heat exchanger becomes the minimum. In other words, it should be noted that when the cascade evaporation temperature is the optimum point, the exergy destruction rate of the R744 compressor and the cascade heat exchanger is minimal. The purpose of this study is to provide basic design data by analyzing the exergy characteristics according to various conditions on the high- and low-temperature side for optimal design of a CRS to which R744 is applied.