Hypersonic vehicles encounter challenges in adapting to complex external environments during missions. Conventional fixed-wing aircraft have limited optimal aerodynamic performance under specific conditions. In contrast, morphing aircraft can adapt to various mission environments by altering their aerodynamic shape to control their flight characteristics. Based on numerical simulations, this paper analyzes the changes in aerodynamic characteristics of a hypersonic folding-wing aircraft before and after wing folding, revealing the effects of wing folding on aerodynamic performance. Meanwhile, the influence of aeroelasticity in the wing on the aerodynamic characteristics of the aircraft during the wing folding process is discussed. The outcomes show that the wing folding process has a minimal effect on the drag coefficient but significantly affects the lift coefficient and lift-to-drag ratio. Moreover, due to the presence of shock waves at the wingtips, stress is mainly concentrated in these areas, resulting in a relatively small impact of aeroelasticity on the aircraft’s aerodynamic behavior.