The invention discloses a control method of a vehicle-mounted air conditioner system and the vehicle-mounted air conditioner system. The control method comprises the following steps that S1, command information of the set temperature of a user is received, and real-time electric quantity of a storage battery, the internal environment temperature inside a compartment and the external environment temperature outside the compartment are detected; S2, a first set operation frequency is selected according to the detected real-time electric quantity, a second set operation frequency is selected according to the set temperature, a third set operation frequency is selected according to the internal environment temperature, a fourth set operation frequency is selected according to the external environment temperature, the first set operation frequency, the second set operation frequency, the third set operation frequency and the fourth set operation frequency are compared to obtain the minimum operation frequency, and the real-time operation frequency of a compressor is adjusted to the minimum operation frequency; and S3, the real-time operation frequency of the compressor, the rotation speed of an indoor fan and the rotation speed of an outdoor fan are adjusted according to the proportional relation between the real-time electric quantity and the total charging capacity of the storage battery. By the adoption of the control method of the vehicle-mounted air conditioner system, energy consumption of the vehicle-mounted air conditioner system can be reduced.