Abstract: Aiming at the problem that the traditional tracking algorithm has large amount of calculation and low accuracy while tracking near space hypersonic target, a kind of variable structure multiple model tracking algorithm was proposed. Established a kind of variable probability and variable model number target model on the basis of analyzing the traditional tracking algorithm, identified the target flight phase with the target motion state identification method, and selected the appropriate filter model and the model transition probability to realize variable structure multiple model tracking. The Monte Carlo simulation results show that, the new algorithm can realize tracking the near space hypersonic vehicle effectively, and the tracking performances are superior to the traditional variable structure multiple model tracking algorithm, it has certain practicability and popularization.