An apparatus for controlling a hybrid vehicle is provided. The apparatus includes an engine generating power by combustion of fuel, a driving motor assisting power of the engine and selectively operated as a power generator to generate electric energy and a clutch disposed between the engine and the driving motor. A battery supplies electric energy to the driving motor and charges the electric energy generated in the driving motor. A plurality of electric superchargers are installed in a plurality of intake lines, in which outside air supplied to combustion chambers of the engine flows, respectively and a controller variably adjusts an operating point of the engine.