The adaptive backstepping method has strong performance in handling control problems with disturbances in previous research. However, it exhibits limitations when applied to time-varying disturbances. This paper proposes an improved adaptive backstepping method based on Discrete Fourier Transform (DFT). By estimating the frequency spectrum of the disturbance and indirectly obtaining its time-domain estimate, the proposed method effectively overcomes the shortcomings of traditional adaptive backstepping. To address the issue of frequency leakage caused by discontinuities in window data, the idea of DFT is improved by using STFT with the addition of the window function and window-shifting operation. Additionally, a projection operator and adaptive reduction of the control objective are employed to mitigate the effects of actuator saturation. Finally, in simulations involving an aircraft subjected to gusts and turbulence, the proposed method is compared with traditional adaptive backstepping and radial basis function (RBF) neural network control methods. Simulation results demonstrate that the proposed method outperforms the others in these experimental scenarios.