Because of the complexities of target motion features, the tracking of hypersonic target in near space is difficult. In this paper, a new adaptive tracking algorithm based on dynamic model and improved square-root cubature Kalman filter(SRCKF) is proposed. According to the target movement characteristics, the improved adaptive piecewise constant Jerk model is proposed based on the dynamic model. The improved square-root cubature Kalman filter which the model mismatch detection function is introduced to reduce the state estimation error. The simulation results indicate that the proposed method which combines the model and the estimation algorithm has higher accuracy and stability on maneuvering target tracking than other existing methods. The research provides a feasible solution to the further improvement of the real time tracking accuracy of near-space hypersonic target.