An apparatus of controlling a vehicle and a method thereof are provided. The operating region of an engine is operated with theoretical air-fuel ratio. The apparatus includes a supercharger that supplies compressed air to a the combustion chamber of the engine and a spark plug that ignites mixed air supplied to the combustion chamber. An intake valve selectively opens and closes the combustion chamber for inflowing the mixed air therein. A variable valve apparatus adjusts an opening timing and closing timing of the intake valve and a controller adjusts an ignition timing of the spark plug and the closing timing of the intake valve through the variable valve apparatus based on the operating region of the engine.