A control apparatus of an engine may include a variable valve lift apparatus, an engine including a plurality of cylinders generating power by combustion of fuel, at least one intake valve and at least one exhaust valve for opening and closing the cylinder, a variable valve lift apparatus adjusting a valve lift of the intake valve and exhaust valve, and a controller driving the intake valve in a low lift mode by using the variable valve lift apparatus and closing the exhaust valve when one of the cylinders among the plurality of cylinders may be deactivated.