An apparatus for controlling an engine includes an engine including a plurality of combustion chambers for generating driving torque by burning a fuel, a high-capacity turbocharger including a turbine rotated by the exhaust gas exhausted from the combustion chambers and a compressor rotated together with the turbine for compressing exhaust gas exhausted from the combustion chamber, an electric supercharger including a motor and an electric compressor operated by the motor, a throttle valve for adjusting an intake air amount supplied to the combustion chamber, a driving information detector for detecting driving information including a required torque and an engine speed, and a controller for determining a driving region of the engine from the driving information detected by the driving information detector, and controlling engine torque by adjusting an opening of the throttle valve and an output of the motor according to the driving region of the engine.