An internal combustion engine includes a plurality of cylinders, a plurality of fuel injection valves, a control chamber provided in each of the fuel injection valves. A control system for the internal combustion engine includes an electronic control unit which is configured to (i) reduce a pressure of the fuel in the control chamber to be lower than a pressure of the fuel in the fuel passage connected to the control chamber, in each of the fuel injection valves, (ii) reduce the pressure of the fuel such that a first pressure difference is equal to or larger than a predetermined pressure difference, so as to move the needle in a direction to open the injection holes, and (iii) reduce the reference pressure by reducing the pressure of the fuel in a second injection valve, such that the first pressure difference after operation is smaller than the predetermined pressure difference.