Fault detection and isolation are very important to improve the UAV navigation accuracy and reliability. The residual chi square algorithm is poor sensitive for small values of soft fault and improved SPRT algorithm can't judge the ending time of the fault, so this paper presents an integrated fault detection algorithm. If the residual chi square algorithm determined the fault ending, the improved SPRT algorithm detection value is corrected on time. As a result,the improved SPRT algorithm can detect faults after the first time. Because of the improved SPRT algorithm is of high sensitivity to fault and residual chi square algorithm can accurately distinguish the fault ending time, the simulation results show that this integrated algorithm has good detecting effection for small values of soft fault or large values step fault. Therefore, this integrated algorithm can effectively improve the ability and sensitivity of the system fault detection and enhance the reliability of the integrated navigation system.