A control apparatus for an internal combustion engine including a supercharging device, which includes: a valve-drive mechanism that variably controls the valve timings for at least intake valves; a target valve timing setting mechanism setting a target valve timing for at least the intake valves in accordance with an operation condition of the engine in a low engine speed range; and a valve-drive mechanism controller controlling the valve-drive mechanism based on the target valve timing. Each of the target valve timings is differently set such that (a) a valve-overlap duration is provided in a negative pressure region; (b) the valve-overlap duration in the negative pressure region is made shorter in a first supercharging region; and (c) the valve-overlap duration in the first supercharging region is made longer in a second supercharging region where the higher load of the engine is required.