The whitening processing by Principal Component Analysis(PCA) may inaccurately estimate the signal subspace dimension without considering the noise impact. This paper proposes a blind signal separation algorithm based on improved whitening by Minimum Description Length(MDL) for estimating the source signal number. It determines the subspace dimension based on the source signal number estimation, and distinguishes between signal and nosie subspace. It can improve the separation performance. The eigenvalues of signal will be corrected by noise average variance estimation,thus it can reduce the impact of noise. Simulation results show that the exact estimate probability by MDL will approach to 1 at hyper-5dB SNR,and the separation performance of improved whitening MDL Fast Independent Component Analysis(FastICA) algorithm can be improved distinctly compared with that of traditional FastICA algorithm.