The invention belongs to the technical field of automobiles, and particularly relates to a control method of a vehicle-mounted air conditioner and a control system of the vehicle-mounted air conditioner. The control method of the vehicle-mounted air conditioner comprises the following steps of: acquiring the estimated vehicle-using time of a vehicle user, and triggering to acquire the current temperature and the current humidity in the vehicle; acquiring an adjusting time prediction function of the vehicle-mounted air conditioner and a target temperature and target humidity of the vehicle user; according to the current temperature, the current humidity, the target temperature and the target humidity, calculating to obtain a predicted operation time by adopting the adjusting time predictionfunction; and starting the vehicle-mounted air conditioner in advance of the predicted operation time relative to the predicted vehicle-using time. According to the control method and the corresponding system, the optimal target temperature and the optimal target humidity can be preset for each vehicle user through the preset adjusting time prediction function, so that the target temperature value and the target humidity value which accord with the habits of the vehicle user can be achieved in less time under the condition of energy conservation, and more comfortable humanized service is provided.