An apparatus for controlling an ABS of an ESC integrated brake system and a method thereof. The apparatus includes a main master cylinder generating hydraulic brake pressure through a piston that is moved forward/backward by an actuator that is operated when a brake pedal of a vehicle is pressed down; and a controller controlling forward/backward movement direction change of the piston by controlling a driving current that is applied to the actuator by determining whether a direction change condition according the control state of wheel pressure is satisfied, when a brake mode of the vehicle is an ABS mode and the piston has reached a predetermined direction change position for forward/backward movement direction change.