A method and system for controlling a hybrid vehicle equipped with an air control valve are provided. The method includes collecting road information and determining a number of conversions between an engine operation mode and a motor driving mode based on the collected road information. Further, a degree of flap closing of the air control valve is restricted from being corrected when the predicted number of conversion is less than a predetermined threshold. The air control valve is adjusted for flap displacement upon closing of the flap when the predicted number of conversion is greater than the predetermined threshold and in which the degree of flap closing of the air control valve is corrected based on the detected flap displacement.