Variant aircraft is one of the typical applications of switched systems. A zonotopic estimation method for uncertain switched systems with asynchronous switching is proposed in this article because the influence of external disturbance and parameter perturbation widely exists in the flight process of variant aircraft. On the basis of a designed robust observer, the states, errors, disturbances, and uncertain parameters are all described with zonotopes. The ultimate estimation is also derived by utilizing the center vector and generator matrix of zonotope. This method solves the problem of obtaining state information of variant aircraft during flight. Moreover, the interval estimation is verified to be bounded via P-radius definition of zonotope and robust stability theory, and the global optimization of the performance is achieved during the estimation process. Finally, a direct method is used to decrease the computing time and improve the estimation accuracy. The methodology is illustrated to be effective through a simulation of the variant aircraft system.