A control system is provided in an internal combustion engine in which a valve timing such as an opening time point and lift amount of an intake valve can be switched to a low-speed or high-speed valve timing within a lean-burn control range established in accordance with the operational state, such as an intake pipe internal absolute pressure and an engine revolution number of the engine, wherein an air-fuel ratio of an air-fuel mixture supplied to the internal combustion engine is enriched for a predetermined time when the valve timing is switched from the low-speed valve timing to the high-speed valve timing while carrying out a lean-burn control. Thus, even when the valve timing is switched over to the high-speed valve timing, the lean-burn control is carried out to prevent a misfiring or an unstable combustion state caused when the valve timing is switched during the lean-burn control, thereby providing a reduction in emission and an enhancement in drivability, while enhancing the specific fuel consumption.