In frequency domain ICA, the frequency bin permutation problem falls off the quality of separated signals. In this paper, we propose a new algorithm to solve the frequency bin permutation problem using the covariance of power ratio of separated signals in multi-channel FD-ICA. It makes use of the continuity of the spectrum of speech signals to check if frequency bin permutation occurs in the separated signal using the power ratio of adjacent frequency bins. Experimental results have shown that the proposed method could fix the frequency bin permutation problem in the multi-channel FD-ICA.