A control system which is applied to an internal combustion engine (1A, 1B), the internal combustion engine (1A, 1B) including: a compressor which is provided in an intake passage; an electric motor which is capable of driving the compressor; a bypass passage which connects a first section of the intake passage, the first section being positioned upstream more than the compressor, and a second section of the intake passage, the second section being positioned downstream more than the compressor; a bypass valve which is provided in the bypass passage; an EGR passage which connects the first section positioned upstream more than the compressor, and an exhaust passage; and an EGR valve which is provided in the EGR passage, wherein the control system includes a control device which is configured to: when a predetermined pressure accumulation condition where a gas flow rate of a specific place (Ps) of the second section positioned downstream more than the compressor, has become less than a rated flow of the compressor, is satisfied, first execute a pressure accumulation control to close the bypass valve and make the electric motor drive the compressor; and then, when a predetermined opening condition is satisfied during an execution of the pressure accumulation control, open the bypass valve and, if the EGR valve is closed, open the EGR valve, wherein the control device is configured to determine that the predetermined opening condition is satisfied in a case where a pressure of gas accumulated in a section lying downstream more than the compressor due to the pressure accumulation control has become equal to or greater than a pressure with which condensed water in the EGR passage is blown off to the exhaust passage when the gas accumulated is led into the EGR passage. a compressor which is provided in an intake passage; an electric motor which is capable of driving the compressor; a bypass passage which connects a first section of the intake passage, the first section being positioned upstream more than the compressor, and a second section of the intake passage, the second section being positioned downstream more than the compressor; a bypass valve which is provided in the bypass passage; an EGR passage which connects the first section positioned upstream more than the compressor, and an exhaust passage; and an EGR valve which is provided in the EGR passage, wherein the control system includes a control device which is configured to: when a predetermined pressure accumulation condition where a gas flow rate of a specific place (Ps) of the second section positioned downstream more than the compressor, has become less than a rated flow of the compressor, is satisfied, first execute a pressure accumulation control to close the bypass valve and make the electric motor drive the compressor; and then, when a predetermined opening condition is satisfied during an execution of the pressure accumulation control, open the bypass valve and, if the EGR valve is closed, open the EGR valve, wherein the control device is configured to determine that the predetermined opening condition is satisfied in a case where a pressure of gas accumulated in a section lying downstream more than the compressor due to the pressure accumulation control has become equal to or greater than a pressure with which condensed water in the EGR passage is blown off to the exhaust passage when the gas accumulated is led into the EGR passage.