A control system for an internal combustion engine, which is capable of reducing exhaust emissions during and after the start of the engine. A control system is capable of changing the valve-closing timing of intake valves relative to the valve-opening timing thereof as desired using a variable intake valve actuation assembly. The control system includes an ECU. The ECU sets a target auxiliary intake cam phase to a start value that sets the valve-closing timing of the intake valves to retarded-closing timing, during starting of the engine, and to a catalyst warmup value that sets the same to timing closer to timing in the Otto cycle operation, during catalyst warmup control after the start of the engine.