Based on the SINS/CNS/GNSS integrated navigation computer, this paper proposes a fault-tolerant integrated navigation computer. First, this paper introduces the main purpose and design thought of the fault-tolerant integrated navigation computer ,and proposes the structured flowchart of the fault-tolerant integrated navigation computer. Secondly, based on the different power consumption of hardware components, this paper designs different hardware fault-tolerance method .Thirdly , based on hardware fault-tolerance, this paper designs the N-version programming method and recovery-block method to realize the software fault-tolerance .Finally, this paper compares the fault-tolerant navigation computer with the traditional navigation computer from two aspects: the utilization of navigation source and the availability of navigation computer. Compared with the traditional navigation computer, the practical application results show that the fault-tolerant navigation computer can effectively monitor and isolate the fault and improve reliability and availability of the integrated navigation computer.