A control system for an internal combustion engine where when the engine is decelerating the amount of intake air supplied to a combustion chamber is controlled. A target auxiliary intake air amount SAIRCMD necessary for preventing misfiring of the engine by supplying only an auxiliary intake air amount to a combustion chamber and a target intake air amount GAIRCMD which is a target value of the amount of intake air supplied to the combustion chamber are calculated according to the state NE, AP of the engine. When the engine is decelerating, and misfires, misfire avoidance control is executed controlling an auxiliary intake air amount control valve to be more opened such that the auxiliary intake air amount becomes the target auxiliary intake air amount SAIRCMD and a throttle valve to be more closed such that the amount of intake air supplied to the combustion chamber becomes the target intake air amount GAIRCMD.