A method for controlling intake and exhaust valves of an engine includes: controlling, by an intake continuous variable valve timing (CVVT) device and an exhaust CVVT device, opening and closing timings of the intake valve and exhaust valves; determining, by a controller, a target opening duration of the intake and exhaust valves 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, current opening and closing timings of the intake valve and/or exhaust valve based on the target opening duration; and advancing or retarding, by the intake and/or exhaust CVVD devices, the current opening timing of the intake and exhaust valves while simultaneously retarding or advancing the current closing timing of the intake and exhaust valve by a predetermined value based on the target opening duration.