The unsteady aerodynamic effects on the flight performance of morphing aircraft remain unclear. The unsteady aerodynamic characteristics during morphing were investigated, and their impact on flight performance was quantitatively analyzed. A dynamic model incorporating unsteady aerodynamic effects was established, with morphing rate and flight velocity as key parameters. A qualitative comparison was conducted between the flight performance under unsteady and quasi-steady aerodynamic models. Two typical flight scenarios were designed, and the pseudo-spectral method was employed to quantify the influence of unsteady aerodynamic effects on mission performance in maximum range operations and no-fly zone avoidance. The results indicate that the unsteady 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 1800m accumulates within 250s. In contrast, maximum range operations exhibit a smaller deviation of around 350m over 1000s of flight.