Abstract: How to precisely estimate and calibrate the systematic errors in the measurements is a key problem for improving the performance of autonomous navigation for satellites using(measurements) of the Earth,the Sun and the Moon.A two-step filter algorithm is designed and(applied) to estimate orbital parameters and identify the measurement biases simultaneously.(Simulation) results show that the 3-σ accuracies for position can be improved to the order of(300m) from the order of 10km using the filter algorithm presented.