The fault detection and exclusion (FDE) algorithm played a very important role in the Wide Area Augmentation System (WAAS). When the WAAS was not available, the FDE algorithm could provide the monitored information for the navigation position solution. It could autonomously provide the integrity monitoring for the position solution, which it had a capability to detect and prevent a positioning failure that affected the navigation. An optimizing evaluation of estimation method was employed in detecting and isolating the outlying measurements for the satellite ephemeris error and the satellite clock error, which could assess the integrity risk in the WAAS. Therefore this algorithm could provide more precise integrity parameters of the satellite ephemeris error and clock error, which the method is more suitable at the master station for engineering application about the satellite.