A method for controlling intake and exhaust valves of an engine may include: determining, by a controller, a target opening duration of the intake and exhaust valves according to a control region determined based on an engine load and an engine speed; modifying, by an intake continuous variable valve duration (CVVD) device and by an exhaust CVVD device, opening and closing timings of the intake valve and exhaust valve based on the target opening duration of the valves; and advancing or retarding, by the intake and/or exhaust CVVD devices, the opening timing of the intake and exhaust valves while simultaneously retarding or advancing the closing timing of the intake and exhaust valve by a predetermined value based on the target opening durations. In particular, the controller classifies five control regions based on the engine load and speed.