In a system for controlling an internal combustion engine having a plurality of cylinders and connected to the automatic transmission and mounted on a vehicle and the operation of the engine is switched between full-cylinder operation during which all of the cylinders are operative and cutoff-cylinder operation during which some of the cylinders are non-operative, based on at least the load of the engine, a gradient of road on which the vehicle runs is estimated and the cutoff-cylinder operation is prohibited when the estimated gradient is equal to or greater than a threshold value. With this, it becomes possible to generate sufficient deceleration, when the vehicle runs a downhill during cutoff-cylinder operation, while ensuring to prevent the operator to feel excessive acceleration.