Abstract: Navigation algorithm for constellation autonomous navigation using inter-satellite measurement is discussed. Considering the characteristic of autonomous system, the algorithm must be provided with ability to check fault points and resist gross errors. Therefore, a scheme of robust estimation based on robust least square estimation and applied on net of inter-satellite measurement is designed in this paper by analyzing the characteristic of net of inter-satellite measurement. According on the difference of influence imposed on residual by fault points and gross errors of observation, the method of processing step by step is put forward. Compared several general schemes of robust estimation by examples, the result shows that!the scheme of robust estimation designed in this paper is effective.