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; retarding an intake valve closing (IVC) timing and limiting a valve overlap between an intake valve and an exhaust valve in a first control region; advancing the IVC timing and applying a maximum duration to the exhaust valve in a second control region; advancing the IVC timing according to an increase of the engine load in a third control region; controlling a throttle valve to be fully opened and advancing the IVC timing in a fourth control region; and controlling the throttle valve to be fully opened and retarding the IVC timing in a fifth control region.