In view of the problem that the traditional single model can not track the near space hypersonic targets effectively, a modified coordinate turn (MCT) model was proposed. According to the characteristics of near space hypersonic targets while skip flying in cruise segment, assuming that the target angular velocity for singer process, with the help of the thought of "current" statistical model, revise the target angular velocity for real-time, combine with the extended Calman filtering algorithm to achieve stable tracking. The Monte Carlo simulation results show that the new model can achieve tracking skip flying near space hypersonic target accurately in the cruise segment, and with more stability of the tracking performance and stronger practicality.