A channel estimation apparatus and the method thereof are disclosed. The channel estimation apparatus includes a time-domain-axis channel estimation unit, a peak-detection module, a first-shift unit, a frequency-domain-axis channel estimation unit and an optimal shift searching module. The time-domain-axis channel estimation unit is used for performing the channel estimation in the time domain so as to obtain initial channel frequency responses by estimating. The peak-detection module is used for outputting a peak information. The shift-optimal-searching module decides the optimal shift information according to the peak information, a feedback signal and entire channel frequency responses. The first-shift unit is used for adjusting the positions of the initial channel frequency responses in the time domain according to the optimal shift information. The frequency-domain-axis channel estimation unit is used for performing the channel estimation in the frequency domain so as to obtain the entire channel frequency responses by estimating.