A method and apparatus for separating a multi-channel mixed signal are provided. The method includes the steps of: a) transforming a temporal domain to a frequency domain by performing a discrete Fourier transform onto at least one of mixed signals inputted from an external device through multi-channel; b) estimating multi-decorrelation by calculating a plurality of cross power spectra for the mixed signal in the transformed frequency domain; c) estimating a separation coefficient of the mixed signal based on relative optimization in order to decorrelate the calculated cross power spectra, where the separation coefficient is serially updated; d) transforming the frequency domain to the temporal domain by performing an inverse discrete Fourier transform on the estimated separation coefficient in the temporal domain; and e) separating an original signal from the mixed signal by filtering the mixed signal using the separation coefficient of the transformed temporal domain.