A method for controlling an exhaust gas recirculation (EGR) system which is provided with an intake throttle valve and an EGR valve driven by a motor may include detecting an engine speed and an amount of intake air for each cylinder of an engine while the engine is operating, determining an amount of air flow supplied to the engine based on the engine speed and the amount of intake air for each cylinder, determining an equivalent cross-section of the EGR valve based on the amount of air flow, determining an opening angle of the EGR valve based on the engine speed, the amount of intake air for each cylinder, the amount of air flow, and the equivalent cross-section of the EGR valve, and controlling the EGR valve according to the opening angle of the EGR valve.