In the navigation based on the federated filter, the fault subsystem is isolated entirely on the fault-detected epoch, without considering the asymptotic changing and components difference of soft fault influence. Therefore, a kind of adaptive fault-tolerant algorithm based on sequential probability mapping for the integrated navigation is proposed. The statistic model of local estimation states is built by fault dynamic mapping. Then the quality of local estimation states under soft fault is calculated online by sequential probability ratio test and finally used in adaptive tuning of global fusion. The simulation results show that the proposed algorithm can improve the falut-tolerant performance under soft fault significantly.