The hypersonic target in near space has the characteristics of high maneuverability, high speed and high nonlinearity,which usually result in some problems in the process of target tracking, such as the reduced tracking accuracy and the filter diverging. To solve the problems, an interactive multiple model cubature particle filter algorithm is proposed. This algorithm uses the interactive multiple model algorithm to track the hypersonic target in near space, and uses the cubature particle filter algorithm to predict the state. The simulation results show that, compared with the interactive multiple model Kalman filter algorithm and interactive multiple model particle filter algorithm, this algorithm has better tracking performance for the hypersonic target in near space.