A method for controlling valve timing of an engine may include: classifying control regions; applying a maximum duration to an intake valve and controlling a valve overlap in a first control region; applying the maximum duration to the intake valve and an exhaust valve in a second control region; controlling a manifold absolute pressure (MAP) of an intake manifold to be maintained constant in a third control region; controlling a wide open throttle valve (WOT) and creating a valve overlap by reducing interference of exhaust in a fourth control region; and controlling a wide open throttle valve (WOT) and controlling an intake valve closing timing based on the engine speed. In particular, the control regions are classified by a controller based on an engine load and an engine speed compared with predetermined values, respectively.