An apparatus for controlling a multi-winding motor may include: a current detector configured to detect currents of a plurality of windings, each of the windings associated with a corresponding rotor; an abnormal determiner configured to determine abnormality of at least one of the plurality of windings on the basis of the currents of the plurality of windings; a compensation calculation unit configured to calculate a current phase offset and/or compensation current of each of the plurality of windings according to the determined abnormality; and a signal output unit configured to output control signals to control at least one of the plurality of windings according to the current phase offset and/or the compensation current.