In order to separate the confused targets spots in the process of the detection of underwater vehicle, use multi-hypothesis track algorithm which was based on Kalman filter theory in application of multi-targets track association. The basic process and principle of multi hypothesis method were introduced in this paper. The basic process included the generation of hypothesis, the calculation of probability and the hypothesis deleting. Simulation experiment proved that multi-hypothesis track algorithm can effectively solve the measurement target data association problem. The target track can also be affirmed in short time.