At present, China’s high-speed rail is in a period of rapid development. Most of the refrigerants used in Chinese motor train units at this stage are still R134a and R407c, which have an impact on the environment. In response to the environmental protection concept of green travel, it is of great significance to study the air conditioning system of motor train units using CO2 refrigerant. Using CFD simulation analysis technology, the heat transfer performance of the air side of the CO2 finned tube evaporator used in the air conditioning system of the motor train unit is studied. We select the air outlet temperature, pressure drop, heat transfer factor, and resistance factor as the objective function, in addition, monitoring points are set up in the air flow channel to monitor the turbulent flow field and pipe wall pressure. Our research shows that the cooling capacity of the CO2 evaporator can reach up to 29.76 kW, which can meet the heat exchange required in the air conditioning system of the motor train unit. In order to obtain a better structure and the conditions of the heat transfer effect, structural optimization was conducted. The simulation results demonstrate several trends: (i) With the augment of the air inlet velocity, the cooling capacity of the evaporator increases and the heat exchange effect improves; when the air inlet ve > 2.2 m/s, the effect of continuing to augment ve on heat exchange is weak. (ii) Following appropriate reduction of the diameter of the heat exchange tube, the wind resistance is reduced and the cooling capacity of the evaporator is improved. (iii) With the enlargement of the fin spacing, the turbulent motion in the flow channel can be fully developed, there is a peak in the change in the heat exchange tube area optimization factor, and the optimal fin spacing is between 1.6 mm and 1.7 mm; at this time, the average turbulent kinetic energy of the air side is larger and the turbulent dissipation rate is smaller. These results provide a reference for the practical application of CO2 refrigerant in the motor train unit.