In this paper, a redundancy management system for aircraft is studied, and fault detection and isolation algorithms of inertial sensor system are proposed. Contrary to the conventional aircraft systems, UAV system cannot allow triple or quadruple hardware redundancy due to the limitations on space and weight. In the UAV system with dual sensors, it is very difficult to identify the faulty sensor. Also, conventional fault detection and isolation (FDI) method cannot isolate multiple faults in a triple redundancy system. In this paper, two FDI techniques are proposed. First, hardware based FDI technique is proposed, which combines a parity equation approach with a wavelet based technique. Second, analytic FDI technique based on the Kalman filter is proposed, which is a model-based FDI method utilizing the threshold value and the confirmation time. To provide the reference value for detecting the fault, residuals are calculated using the extended Kalman filter. To verify the effectiveness of the proposed FDI methods, numerical simulations are performed.