A method for controlling valve timing of an engine includes: classifying control regions depending on an engine speed and an engine load, and applying a maximum duration to an intake valve and controlling a valve overlap in the first control region; advancing an intake valve closing (IVC) timing and applying the maximum duration to the exhaust valve in the second control region; advancing both the IVC timing and an exhaust valve closing (EVC) timing in the third control region; fixing an exhaust valve opening (EVO) timing and approaching the EVC timing to a top dead center (TDC) in the fourth control region; controlling a wide open throttle valve (WOT) and retarding the EVO timing in the fifth control region; and controlling the WOT, advancing the EVO timing, and approaching the EVC timing to the TDC in the sixth control region.