The present disclosure provides a system and a method for controlling valve timing of a continuous variable valve duration engine. The method may include: classifying a plurality of control regions depending on an engine speed and an engine load; applying a maximum duration to an intake valve and controlling a valve overlap between the intake valve and an exhaust valve in a first control region; maintaining the maximum duration of the intake valve and applying a maximum duration to the exhaust valve in a second control region; maintaining a manifold absolute pressure (MAP) at a predetermined pressure in a third control region; controlling a throttle valve to be fully opened and generating the valve overlap in a fourth control region; and controlling the throttle valve to be fully opened and controlling intake valve closing (IVC) timing according to the engine speed in a fifth control region.