Abstract: Capability of the active satellite navigation system is to estimate clock and(position) error autonomously.The capability is called as autonomous navigation.The algorithm of estimating the each satellite clock error was focused.Generally,in order to autonomous(navigating),each satellite makes pseudorange measurements to other visible satellites.Then these measurements are cross-linked to every satellites,so each can calculate every clock error.A new method of conditional estimating was introduced to calculate the clock error.The principle and(approach) of the method was discussed in detail.The synchronization error which was the difference between each estimated error was less than 0.4m(RMS).