In a system for controlling an internal combustion engine, first opening determination of determining whether to open an air bypass valve 22 on the basis of a compressor flow rate (target compressor flow rate QAIRCMD) passing through a compressor 17 and a compressor front-rear pressure ratio P2/P1, and second opening determination of determining whether to open the air bypass valve 22 on the basis of an opening ratio reduction amount DRTHO as a reduction amount of an opening ratio RTHO of a throttle valve 13 are performed. The air bypass valve 22 is opened when it is determined in both of the first opening determination and the second opening determination that the air bypass valve 22 should be opened.