The probability of pseudo-range information being faulty will increase when there is increased noise in the receiver due to highly dynamic conditions. In this paper, an intelligent fault-tolerant federated Kalman filter (IFFKF) is presented to solve the problem of invalid position information as a result of the uncertainty in the category and quantity of failed satellites in a multiple configured satellite system. At the same time, a corresponding intelligent fault-tolerant system structure based on a cell-level fusion mode of operation was designed. Furthermore, a fault diagnosis strategy is proposed to deal with gradually or suddenly changing faults. By monitoring the residual and the residual rate, an observation quality gene is obtained using a fuzzy logic control system, and the local filter is adaptively adjusted on-line. Consequently, any filtering divergence arising from a gradually changing fault can, to a large extent, be prevented. The results show that the proposed algorithm and structure can achieve reliable positioning by fully utilizing new multiple satellites, monitoring and managing the gradual fault, as well as detecting and isolating any sudden fault in a synchronous manner. As such, the proposed algorithm has the potential to improve the reliability of a multiple satellite configured navigation system.