A control system for an internal combustion engine, which is capable of enhancing the accuracy of fuel control and ignition timing control even when there is a possibility that the reliability of a calculated intake air amount lowers, and enables reduction of manufacturing costs. An ECU of the control system calculates a first estimated intake air amount according to a valve lift, a cam phase, and a compression ratio, calculates a second estimated intake air amount according to the flow rate of air detected by an air flow sensor. The ECU determines a fuel injection amount according to the first estimated intake air amount when an estimated flow rate Gin_vt calculated based on an engine speed, the valve lift, the cam phase, and the compression ratio is within the range of Gin_vt.ltoreq.Gin1, and according to the second estimated intake air amount when Gin2.ltoreq.Gin_vt.