The tracking and trajectory prediction of axisymmetric hypersonic maneuvering aircraft in near space are discussed. By introducing three state variables related to aerodynamic parameters, a nonlinear maneuver  model is established and the observability of the nonlinear tracking system based on the model is proved. For this nonlinear tracking system, an extended Kalman filter and a state predictor are designed to achieve trajectory tracking and prediction. The simulation results show that the proposed maneuver model achieves excellent tracking and prediction effects for the near space aircraft at the end of the cruise.