A microphone signal compensation apparatus includes a plurality of audio input units to respectively receive a target signal, each audio input unit of the plurality of audio input units including a microphone; a constant filter unit to selectively apply a constant filtering calibration scheme to signals output by the plurality of audio input units to compensate for a difference in at least one characteristic among the audio input units, the constant filtering calibration scheme being estimated from an average value of a ratio of a desired signal to a reference signal among the signals output by the plurality of audio input units; and a noise remover to remove noise from the signals processed by the constant filter unit, and to separate the target signal from the signals from which the noise has been removed.