An apparatus of controlling an engine including an electric supercharger includes: an engine to combust fuel to generate power; a drive motor to assist the power of the engine and selectively operate as a generator to generate electrical energy; a battery configured to supply electrical energy to the drive motor and to be charged by the electrical energy generated from the drive motor; a plurality of electric superchargers respectively installed in a plurality of intake lines through which an ambient air flows to be supplied to a combustion chamber of the engine; and a controller that based on a determined driving tendency, adjusts a target speed of the electric superchargers of the plurality of electric superchargers, determine a driving mode of the electric superchargers, limits a maximum output of the engine, and variably adjusts a SOC electricity-generating region where the engine charges the battery.