An apparatus of controlling a hybrid vehicle may include: an engine; a drive motor to assist the power of the engine and selectively operate as a generator to generate electrical energy; a battery to supply electrical energy; a first intake valve disposed in a first intake line; a second intake valve disposed in a second intake line; a first electric supercharger disposed in the first intake line; a second electric supercharger disposed in the second intake line; a connecting valve disposed in a connecting line for connecting the first intake line and the second intake line; and a controller that determines a driving mode of the first and second electric superchargers. In particular, the controller controls the drive motor and the first and second electric superchargers based on a supercharger consumed energy, an additional fuel energy, and a drive motor consumed energy.