The present disclosure provides a system and a method for controlling valve timing of continuous variable valve duration engine. The method includes: classifying control regions depending on engine speed and engine load; applying a maximum duration to an intake valve and controlling valve overlap between the intake valve and an exhaust valve in a first control region; applying the maximum duration to the intake valve and reducing the valve overlap by using exhaust valve closing (EVC) timing in a second control region; advancing intake valve closing (IVC) timing according to an increase of the engine load in a third control region; controlling a throttle valve to be fully opened and controlling the EVC timing to an angle after top dead center in a fourth control region; and controlling the throttle valve to be fully opened and controlling the IVC timing according to the engine speed in a fifth control region.