A compensation control system is provided for preventing braking inconvenience of a flex brake that compensates for brake hydraulic pressure only for initial braking when a brake mode is forcibly switched, thus allowing a driver to recognize a change in braking force, and thereby improving stability when a vehicle is driven. The control system forcibly switches the brake mode, selected by a driver when a booster system fails, into a normal brake mode, and compensates to reduce the magnitude of brake hydraulic pressure, which is to be reduced when the brake mode is forcibly switched, during initial braking.