The present disclosure provides a system and a method for controlling valve timing of a continuous variable valve duration. The method may include: classifying a plurality of control regions depending on an engine speed and an engine speed; applying a maximum duration to an intake valve in a first control region; maintaining the maximum duration of the intake valve and controlling the exhaust valve to reach a maximum duration in a second control region; advancing intake valve closing (IVC) timing and exhaust valve closing (EVC) timing in a third control region; controlling the IVC timing to be close to bottom dead center (BDC) in a fourth control region; controlling a throttle valve to be fully opened and controlling the IVC timing to an angle after BDC in a fifth control region; and controlling the throttle valve to be fully opened and advancing the IVC timing in a sixth control region.