An apparatus and a method for controlling a hybrid vehicle are provided. The apparatus includes an engine that generates power by combusting fuel and a drive motor that supplements the power from the engine and operates selectively as an electric generator to produce electrical energy. A clutch is disposed between the engine and the drive motor and a battery supplies electrical energy to the drive motor and is charged with the electrical energy produced by the drive motor. Multiple electric superchargers are installed in multiple intake lines through which outside air to be supplied into a combustion chamber of the engine flows. A controller determines an operation mode of the multiple electric superchargers based on required power of a driver and a state of charge (SOC) of the battery and adjusts the power output from the engine and the power output from the drive motor.