Hypersonic aircraft have been rapidly developed in recent years both theoretically and experimentally. Aerothermoelastic simulation is very challenging due to its inherent complexity, but physical tests are a workable approach. Flutter tests with variable speed are a popular alternative to hypersonic tests which provide nonstationary structural response data. This paper proposes a nonstationarity assessment method based on energy distribution in the time-frequency domain. The proposed method reveals the nonstationarity level corresponding to the appropriate modal identification algorithm or flutter boundary prediction (FBP) method. Several classic flutter criteria are utilized to build a hypersonic aircraft FBP framework. Numerical simulation and experimental applications demonstrate the effectiveness and feasibility of the proposed method, which facilitates accurate flutter predictions for the subcritical turbulence response during hypersonic flutter flight.