Disclosed is a method for controlling an electro-mechanical brake system including a cascade controller, in which a position controller, a speed controller and a current controller are integrated to control a motor. The method includes determining whether an actual speed of a motor exceeds a command speed of the motor in an early stage of a motor operation; and restricting speed reduction of the motor until a braking force is generated if the actual speed of the motor exceeds the command speed of the motor in the early stage of the motor operation. Speed reduction of the motor is restricted until braking force is generated even if a speed error (actual speed of the motor>command speed of the motor) occurs in the early stage of the motor operation in the EMB system, thereby improving the braking responsiveness.