A control system of an internal combustion engine provided with a first fuel injection valve that injects fuel into a cylinder of the internal combustion engine, a second fuel injection valve that injects fuel into an intake port of the internal combustion engine, an EGR passage that introduces an EGR gas from an exhaust passage of the internal combustion engine to an intake passage thereof, an EGR valve that is arranged in the EGR passage, and an obtaining unit that obtains an amount of intake air in the internal combustion engine. When the EGR valve is open, a determination is made as to whether the amount of intake air is in an increasing tendency or in a decreasing tendency with respect to a change in the cylinder injection ratio, and a value of the amount of intake air thus obtained is corrected based on the determination.