This invention relates to a control system and method for an in-cylinder injection internal combustion engine, which perform control of the timing of fuel injection, the timing of ignition and an EGR rate to assure the stability of combustion in the engine and also its exhaust gas cleaning performance while promoting an improvement in gas mileage by performing injection in compression strokes. The system is provided with a fuel injection valve for directly injecting fuel into a combustion chamber, a spark plug arranged in the combustion chamber, an EGR valve arranged in an EGR passage, a fuel injection timing control unit for controlling a fuel injection timing of the fuel injection valve on a basis of a preset target fuel injection timing, an ignition timing control unit for controlling an ignition timing of the spark plug on a basis of a preset target ignition timing, an exhaust gas recirculation rate control unit for controlling an opening of the EGR valve on a basis of a preset target EGR rate, and a misfire determination unit for detecting a burning fluctuation, whereby upon detection of a burning fluctuation, the target fuel injection timing, the target ignition timing and the target EGR rate are retarded or decreased.