In a control system of a vehicle air conditioner, when a temperature difference between a previous target air temperature at the previous manual operation and a present target air temperature at the present manual operation is smaller than a predetermined value, that is, when it is estimated that a passenger's desired air amount is not set by the previous manual operation, a blower voltage control characteristic for controlling an air amount of a blower is corrected so that a set value at the previous manual operation is not affected to the present learning. Accordingly, it can prevent air-conditioning feeling from being deteriorated due to mis-learning.