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Full-waveform inversion (FWI) is a powerful tool to reconstruct the complex subsurface geologic structures. A major numerical difficulty of FWI is the presence of local minima in the least-squares misfit. To overcome this problem, we propose a time-windowed and phase-encoded frequency domain FWI scheme. This new approach implements multi-scale strategy both in time domain and in frequency domain. Meanwhile, the encoded simultaneous-source technique is used to reduce the computational cost. Numerical examples prove the validity of this approach.