To optimize the performance of the transcritical CO2 two-stage compression refrigeration system, the energy analysis and the exergy analysis are conducted. It is found that higher COP, lower compression power, and less exergy destruction can be achieved when the auxiliary gas cooler is applied. Moreover, the discharge temperature of the compound compressor (HPS) can be reduced by decreasing the temperature at the outlet of the auxiliary gas cooler (Tagc,out). When the Tagc,out is reduced from 30 to 12 °C, the discharge temperature of the compound compressor (HPS) can be decreased by 13.83 °C. Furthermore, the COP and the exergy efficiency can be raised by enhancing the intermediate pressure. Based on these results, the optimizations of system design and system operation are put forward. The application of the auxiliary gas cooler can improve the performance of the transcritical CO2 two-stage compression refrigeration system. Operators can decrease the discharge temperature of the compound compressor (HPS) by reducing the Tagc,out, and increase the COP and the exergy efficiency by enhancing the intermediate pressure.