The accuracy of autonomous orbit determination of Lagrangian navigation constellation will affect the navigation accuracy for the deep space probes. Because of the special dynamical characteristics of Lagrangian navigation satellite, the error caused by different estimation algorithm will cause totally different autonomous orbit determination accuracy. We apply the extended Kalman filter and the fading–memory filter to determinate the orbits of Lagrangian navigation satellites. The autonomous orbit determination errors are compared. The accuracy of autonomous orbit determination using fading-memory filter can improve 50% compared to the autonomous orbit determination accuracy using extended Kalman filter. We proposed an integrated Kalman fading filter to smooth the process of autonomous orbit determination and improve the accuracy of autonomous orbit determination. The square root extended Kalman filter is introduced to deal with the case of inaccurate initial error variance matrix. The simulations proved that the estimation method can affect the accuracy of autonomous orbit determination greatly.