The non-constant aerodynamic effects on the flight performance of morphing aircraft remain unclear. The non-constant aerodynamic characteristics during morphing were investigated, and their impact on flight performance was quantitatively analyzed. A dynamic model incorporating non-constant aerodynamic effects was established, with morphing rate and flight velocity as key parameters. A qualitative comparison was conducted between the flight performance under non-constant and quasi-constant aerodynamic models. Two typical flight scenarios were designed, and the pseudo-spectral method was employed to quantify the influence of non-constant aerodynamic effects on mission performance in maximum range operations and no-fly zone avoidance. The results indicate that the non-constant aerodynamic model introduces deviations in flight state accuracy compared to the quasi-steady model, which correlate with morphing rate and flight velocity. These deviations predominantly occur in low-altitude, low-speed (below Mach 3) flight regimes. During no-fly zone avoidance, where morphing is more pronounced, a trajectory deviation of approximately 1 800 m accumulates within 250 s. In contrast, maximum range operations exhibit a smaller deviation of around 350 m over 1 000 s of flight.