One of the key problems of brain-computer interfaces (BCI) is low signal-to-noise ratio (SNR) of electroencephalogram (EEG) signals. It affects recognition performance. To remove the artifact and noise, block under-determined blind source separation method based on the small number of channels is proposed in this paper. The non-stationary EEG signals are turned into block stationary signals by piecewise. The mixing matrix is estimated by the second-order under-determined blind mixing matrix identification. Then, the beamformer based on minimum mean square error separates the original sources of signals. Eventually, the reconstructed EEG for mixed signals removes the unwanted components of source signals to achieve suppressing artifact. The experiment results on the real motor imagery BCI indicated that the block under-determined blind source separation method could reconstruct signals and remove artifact effectively. The accuracy of motor imagery task of BCI has been greatly improved.