Abstract: The signal obtained by self-guided torpedo by laser is the backscattering signal of warship wake flow and sea water, from which extracting the backscattering signal of warship wake flow is the key point of realizing the self-guided torpedo by laser. While the backscattering signal of water constantly influences the detection of backscattering optical signal of warship wake flow, and it is stronger than the needed signal, the characteristics of the two signals in time domain and frequency domain are very similar. So the separation of these two signals can not be realized with the traditional method effectively. The blind source separation and independent component analysis theory were used to process the signal obtained by laser detection system, and the experiment data was calculated by the software complied in the independent component analysis ideology. The results show that this method can extract the backscattering signal of wake flow from the original signal effectively in different condition, which can help the system judge the warship wake flow and its characteristics.