Setting values of a fuel injection quantity for an engine having an exhaust gas recirculator (EGR) and variable nozzle turbo (VNT), and an engine speed, and measurement values of a manifold air pressure (MAP) and a mass air flow (MAF) are obtained. According to a combination of the reference values of an EGR valve opening degree and a VNT nozzle opening degree, which correspond to the setting values, or a combination of a control value of the EGR valve opening degree by a MAF controller and a control value of the VNT nozzle opening degree by a MAP controller, which correspond to the measurement values, a mode that the MAF and MAP controllers, a first interference compensator from the MAF controller to the MAP controller and a second interference compensator for the reverse direction are enabled and a mode that the MAF or MAP controller is enable are dynamically switched.