Taking liquid nitrogen filling in fresh-keeping transportation truck with controlled atmosphere for fruits and vegetables as design platform, a kind of control system regarded ARM11 series of S3C6410 microprocessor as the core was developed. In the Linux operating system environment, the system used C language and Qt interface designing language to the temperature, relative humidity, oxygen concentration sensor and actuator signal, such as refrigeration equipment, humidifying equipment, the gas adjustment equipment, ventilation equipment and so on. In the proposed system, a kind of variable air volume ventilation system was designed and a type of fruits and vegetables’ fresh-keeping parameters database was established, meanwhile, the collected data in the process of running would be stored in NAND Flash, so that user could read it in real-time and export it after the test. Test showed that the system could correctly collect the fresh-keeping parameters of fruits and vegetables in the truck, and according to the processing results, it could accurately control the corresponding actuators in time. The design and experiment provided a reference for the design of fresh-keeping transportation truck with controlled atmosphere for fruits and vegetables.