To address the problem that the performance of time error estimatio degrades severely in fast frequency hopping (FFH) satellite communications under malicious interference, a time error estimation method based on interference preprocessing is proposed. The proposed method designs a frequency-domain interference detection and suppression scheme based on segmented FFT, which can effectively detect and suppress interference-affected frequency hopping signals. In addition, a segmented FFT based frequency-domain time error estimation method is employed to achieve reliable time error estimation under different malicious interference conditions. The performance of time error estimation under various interference scenarios is evaluated through simulations. Simulation results demonstrate that the proposed method can achieve accurate estimation under different interference bandwidths and interference power levels, with the mean squared error (MSE) of the normalized time error below 0.01, thereby ensuring the correct demodulation of FFH signals.