Aiming at the problem that the navigation accuracy of integrated navigation system of aircraft decreases due to uncertain faults in high dynamic environment, a fault-tolerant federated filtering algorithm based on vector information assignment was proposed. The fault detection function in vector form was designed to determine the fault degree of each observation, which overcomes the disadvantage of isolating all the observations of the fault subsystem at the same time. According to whether the observations were abnormal, the variable measurement noise matrix and information distribution vector coefficient were reconstructed to distribute the information among the state variables of the sub-filter. While isolating the abnormal observation of the fault subsystem, the correct observation information was utilized to the maximum extent. Simulation results show that the algorithm can give full play to the advantages of each navigation subsystem, greatly improve the utilization rate of navigation subsystem information, and have high accuracy and fault tolerance.