Abstract: A control system for an engine with a mechanical supercharger supercharges intake air. The control system has a valve timing variable mechanism for varying an opening and closing timing of an intake valve, a fuel injector delivering fuel in an intake stroke of each of the cylinders of the engine in a high load and low speed region of the engine, and a controller for controlling the valve timing variable mechanism. In a high load region of the engine, an overlapping period of an intake valve and an exhaust valve is longer in a high speed region than in a low speed region. A closing time of the intake valve is earlier than a predetermined optimum closing time and a closing time of the intake valve in a high speed region is later than in the low speed region.