A system of controlling an engine includes: an engine including a combustion chamber, an intake valve, an ignition switch, and an exhaust valve; a dual continuously variable valve duration device to adjust an intake duration of the intake valve and an exhaust duration of the exhaust valve; and a controller for adjusting an ignition timing of the ignition switch, the intake duration, and the exhaust duration based on a driving condition of the vehicle. In particular, until the temperature of the exhaust gas reaches a predetermined temperature after the engine starts, the controller sets the ignition timing to an ignition timing within a predetermined ignition timing range, sets the intake duration of the intake valve to an intake duration within a predetermined intake duration range, and increases the exhaust duration of the exhaust valve to a limit exhaust duration according to the set intake duration.