Provided is an apparatus and method for protecting an overcurrent of a clutch control system including a motor, an inverter including a plurality of switching elements and configured to convert DC power into AC power by ON/OFF of the plurality of switching elements and to provide the AC power to the motor; a motor control unit configured to detect a current provided to the motor; and a microcomputer having an overcurrent threshold for overcurrent detection set for each of a predetermined number of levels, and configured to compare the detected current with the overcurrent threshold for each level, to diagnose whether there is a level corresponding to an overcurrent, to measure an overcurrent duration when there is a level corresponding to the overcurrent, and to control the inverter based on the overcurrent duration.