The invention discloses an air conditioning system for fresh-keeping transportation of fruits and vegetables, which comprises a liquid nitrogen tank, a liquid nitrogen flow control mechanism, a vaporization device, a signal acquisition module, a human-machine interactive interface and an ECU. The invention also discloses an implementation method for the air conditioning system for the fresh-keeping transportation of the fruits and vegetables, which comprises the following steps of: acquiring signals of a temperature sensor, an oxygen sensor and a pressure sensor; if the monitored oxygen concentration is higher than a set value and the temperature is higher than a set value, starting a liquid outlet pipe electromagnetic valve of the liquid nitrogen flow control mechanism; if the oxygen concentration is higher than the set value or the temperature is lower than or equal to the set value, closing the liquid outlet pipe electromagnetic valve of the liquid nitrogen flow control mechanism; and if the monitored oxygen concentration is lower than or equal to the set value and the monitored temperature is higher than the set value, closing the liquid outlet pipe electromagnetic valve of the liquid nitrogen flow control mechanism. The system and the method have the advantages of high oxygen reducing speed, benefit for balance of temperature field, high intellectualization degree, good fresh-keeping effect, system safety and reliability, high accuracy, good stability and the like.