Through analyzing the whitening and separation process of signal based on natural gradient,a blind source separation algorithm with natural gradient based on whitening process is proposed.The algorithm colligates the whitening and separation of signal,and need not whiten the signal individually.By the application of natural gradient,the performance of algorithm is improved.Deduction proves that the algorithm satisfies the separation,equal variety and nonsingularity of separation matrix.Simulation shows that the algorithm can separate and reconstruct source signal effectively.Compared with the random gradient algorithm without signal’s whitening and the conventional FastICA algorithm,it exhibits faster convergence as well as better separation effect and is more favorable for blind source separation.