The invention discloses a CO2 double temperature freezing system with an ejector, a method and application of the system. The system comprises the ejector and a control loop. When environment temperature is lower than a set value, by adjusting the control loop, gas from an outlet of a medium temperature evaporator and gas from an outlet of a low pressure compressor are mixed without entering the ejector, and are directly mixed with gas from an outlet of a subcooler to enter a high pressure compressor, and at the moment, the system works in a subcritical state; and when the environment temperature is higher than the set value, by adjusting the control loop, the system is operated together with the ejector after automatic switch, gas from the outlet of the subcooler is used as primary flow to enter the ejector, gas from the outlet of the medium temperature evaporator is used as secondary flow to enter the ejector, and the mixed gas enters the high pressure compressor to continue to recycle. The ejector is introduced, the system energy efficiency ratio is improved, the throttling loss is recycled to a certain degree, and CO2 is more efficiently used in China.