An engine system according to an exemplary embodiment of the present invention may include an engine including a plurality of cylinders; a fuel separator separating into a low-octane fuel and a high-octane fuel based on an octane number; a cylinder deactivation device deactivating some cylinders among the plurality of cylinder based on a driving region; a low-octane fuel injector injecting the low-octane fuel separated by the fuel separator into the plurality of cylinder; a high-octane fuel injector injecting the high-octane fuel separated by the fuel separator into the activated cylinders without being deactivated by the cylinder deactivation device; and a controller configured to control the cylinder deactivation device to deactivate some cylinders or activate all the cylinders, and to control the low-octane fuel injector and the high-octane fuel injector to inject the low-octane fuel or the high-octane fuel into the cylinders.