A control system of an internal combustion engine changing an operating timing of a valve in an internal combustion engine where a valve drive cam (13) and a pump drive cam (150) are both provided on a valve camshaft (1) is provided. That control system has a device inhibiting the operating timing from being returned in a direction reverse to the direction of the target operating timing during change of the operating timing. Further, in the control system, the relative rotational phases of the valve drive cam and the pump drive cam are set considering utilization of the composite reaction torque of the valve operation drive reaction torque and the fuel pump drive reaction torque acting on the valve camshaft for changing the operating timing in the direction of the target operating timing.