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Time-varying channel estimation is a well-known challenge for the wireless communications in the high mobility environments. In this paper, we propose a basis expansion model (BEM) based channel estimation algorithm utilizing orthogonal spatial domain subspace projection. The channel estimation is taken on each subspace and the estimation results of all subspaces are combined to obtain the final time-varying channel parameters. In our proposed scheme, the wave number spectrum shifting is utilized to suppress the time-varying level on each subspace and the wave number spectrum recovery is adopted in the combination process. Simulation results are provided to verify our proposed scheme.