Aiming at the characteristics of nonlinearity, strong coupling and maneuvering, parameter varity and unique aerodynamics and so on in hypersonic vehicle, the method of neural network aided Kalman filtering for the near space hypersonic vehicle is proposed, and be applied to study of hypersonic target tracking by synthetically applying military operational research theory and method,system modeling technique, neural network technique and computer simulation technique, etc. The basic thought is making use of study capability of BP neural network to overcome the divergence problem in extended Kalman filter. After the extended Kalman filter, adding an error processing section makes filter concentrated. The simulation study shows that the algorithm is better than ones by extended Kalman filter. The Algorithm will have certain reference in target interception of hypersonic vehicle in Near Space.