The safety and reliability of the measuring elements of an aero-engine are important preconditions of the stable operation of the engine control system. The number of control parameters of a variable cycle engine increases by 20%–40% compared to traditional engines. Therefore, it is important to conduct study on the analytical redundancy, design fault diagnosis and isolation of the sensors, as well as the signal reconstruction system, so as to increase the ratability and fault-tolerant capability of the variable cycle engine control system. The analytical redundancy method relies on the accuracy of the mathematical model of the engine. During the service cycle of the engine, it is inevitable that the engine performance will deteriorate, resulting in a mismatch with the model. In this paper, the adaptive model of the variable cycle engine is built with a Kalman filter. Based on this, the strategy of analytical redundancy logic is built and the dynamic adaptive calculation of the threshold is introduced. Simulation results reflect that this method can effectively increase the reliability of sensor fault diagnosis and the accuracy of the analytical redundancy when there is performance degradation of the variable cycle engine.