An EGR system control method of an engine may include calculating a target mass flux ({dot over (m)}egrd) of EGR gas flowing an EGR line, calculating an effective flowing area (EFA) of an EGR valve disposed on the EGR line, calculating an EGR flow sensitivity by dividing the target mass flux with the effective flowing area, and controlling a real opening rate of the EGR valve by applying the EGR flow sensitivity to a target opening rate of the EGR valve. Accordingly, a gain value is varied on a real time according to an effective flowing area of the EGR valve and a target mass flux of EGR gas such that real opening rate of an EGR valve is accurately and precisely controlled.