A control system of an internal combustion engine in which a first fuel of ammonia and a second fuel which is easier to burn than ammonia are used as fuels. An ammonia ratio is usually set to a reference ammonia ratio which is determined in advance in accordance with an operating state of an engine. At the time when feed of the fuel is restarted after suspension of feed of the fuel at the time of deceleration, the ammonia ratio is temporarily made lower than the reference ammonia ratio in accordance with the operating state of the engine.