Aeroelastic stability of the wing is analyzed by taking a low-aspect-ratio wing during supersonic cruise as an example. A hierarchical solution was processed to solve the temperature filed in transient thermal environment, normal mode and flutter boundary in supersonic regime according to time sequence. For a low-aspect-ratio wing with fully-fixed supported conditions in the root chord, the natural frequency can be raised at the beginning of aerodynamics heating. However, the structural natural frequencies are lowered as the aerodynamics heating proceeds, especially the torsional mode frequency, which directly lowers the bending and torsion mode coupling frequency, subsequently lowering the aircraft’s flutter boundaries. Different constraint conditions have different effects on the change of thermal stress; the fewer constraints are in the root, the less the overall structural stiffness or flutter boundaries change.