For hypersonic-vehicle fairing separation, the reliable separation of the fairing and rapid suppression of the separation disturbance are required in scenarios where there is high dynamic pressure and there are abrupt changes in the aerodynamic shape of the aircraft as well as overall parameters. A switching-based control method is proposed in this paper for the interference suppression of hypersonic-vehicle fairing separation, aiming to ensure the stability of the control system in cases of abrupt changes in the controlled object. First, an unsteady-flow calculation method is adopted to clarify the aerodynamic interference characteristics of the aircraft in fairing separation, and the aerodynamic calculation model of the hypersonic-vehicle fairing-separation process is established; then, two states of the aircraft, with and without fairing, are transformed into a subsystem with switching characteristics. The attitude-stability problem in the fairing-separation process is transformed into a problem of solving the arbitrary switching of the switched system by using the linear matrix inequality (LMI) approach. Meanwhile, the control system for interference suppression of the fairing separation is designed by considering the aerodynamic interaction of the fairing movement with the aircraft during the separation. The simulation results showed that the designed control system can realize the reliable separation of the fairing under high dynamic pressure and effectively suppress interference in the separation process.