The present invention provides a control system and method of a vehicle-mounted air conditioner. The system comprises a signal detection device, a signal processing device, a control device and an executive device; the signal detection device is used for detecting physiological data of users and transmitting a physiological data signal to the signal processing device; the signal processing device is a vehicle-mounted entertainment system and used for receiving the physiological data signal, determining physiological status of the users, and transmitting a physiological status signal to the control device; the control device is a vehicle-mounted air conditioner controller and used for receiving the physiological status signal and calculating set values of air volume, temperature, air-out mode and air-intake mode of the vehicle-mounted air conditioner; and the executive device is a vehicle-mounted air conditioner adjusting part and used for adjusting part arrangement of the air conditioner according to the set values of the air volume, temperature, air-out mode and air-intake mode of the vehicle-mounted air conditioner. An in-car comfortable environment suitable for physical status is built for the users, the users are not required to manually participate in the adjusting process, operation of the users is reduced, attention of a driver is ensured, and intelligence of the automotive air conditioner is increased.