A control system is applied to an internal combustion engine. The internal combustion engine includes an electric compressor provided in an intake passage, a bypass passage which bypasses the electric compressor, a low pressure EGR passage which connects a section of the intake passage, which is positioned upstream more than the electric compressor, and an exhaust passage, and a low pressure EGR valve provided in the low pressure EGR passage. An ECU, when a predetermined pressure accumulation condition where a gas flow rate of a specific place of the intake passage has become equal to or less than a predetermined amount, is satisfied, first executes a pressure accumulation control where the bypass valve is closed and the electric compressor is activated, and then, when an opening condition is satisfied during an execution of the pressure accumulation control, opens the low pressure EGR valve and opens the bypass valve.