Turbine-based combined cycle (TBCC) engines are one of the ideal powers for reusable air-breathing supersonic aircraft, but the flight/propulsion integrated control and mode transition restricts its use. This paper takes the Mach 4 over-under TBCC engine as the research object. The inlet is established by the quasi-one-dimensional calculation theory, which can reflect the shock wave position. An iterative method is proposed, which points out that the flow rate in the mode transition depends on the flow capacity. By connecting the input and output that affect each other, the simulation of the coupling characteristics of the aircraft and engine are realized. A GA-LQR-based controller design method is proposed and verified through the aircraft’s climb and mode transition conditions. The simulation shows that the integrated control system can ensure the stability of the aircraft and the safe operation of the engine in the above two situations. During the mode transition process, the aircraft altitude and Mach number fluctuate less than 1%, and the normal shock wave of inlet is in a safe position.
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