A low computational complexity blind channel identification algorithm based on FFT was proposed for short burst signal. This algorithm was expoliting the property of the MCR algorithm only requiring minimum redundancy information to obtain the channel vector,then made the linear equations established by MCR algorithm through FFT to get the channel vector, a fast order estimation algorithm was proposed by expoliting the rank information of matrix .The simulation proved that the proposed algorithm could overcome the shortcoming of the traditional identification algorithms in condition of small observed data and reduce the computational complexity of the original FFT-based algorithm with improved robustness to order.