There is provided a system for controlling an intake valve of an internal combustion engine, including a variable valve mechanism having a control shaft to continuously vary a valve lift amount of the intake valve according to a rotational angle of the control shaft and an actuator to drive the control shaft, and a control unit that controls the actuator so as to set the control shaft to a first rotational angle position at which the valve lift amount takes a first value during an engine idling period and to a second rotational angle position at which the valve lift amount takes on a second value larger than the first value to provide a required intake quantity to start the engine during a time from the beginning of an engine speed decrease period, through an engine stop period, until the completion of a cranking period of the engine.