The present disclosure provides a system and a method for controlling valve timing of a continuous variable valve duration engine, including: classifying a plurality of control regions based on engine load and speed; applying a maximum duration to an intake valve and a long duration to an exhaust valve in a first control region; maintaining a maximum valve overlap in a second control region; advancing intake valve closing (IVC) timing and exhaust valve closing (EVC) timing in a third control region; applying a short duration to the exhaust valve and controlling the IVC timing to bottom dead center 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 applying the long duration to the exhaust valve, and controlling the IVC timing to prevent knocking in a sixth control region.