This paper use three methods to restrain the noise of fluxgate magnetometer,efficiently  remove the geoelectric noise of geomagnetic data of Pi Xian geomagnetic observatory. The three methods are：wavelet threshold filtering and empirical mode decomposition filtering and wavelet threshold filtering based on empirical mode decomposition. At last we contrast the result with Wu Han geomagnetic  observatory which without geoelectric noise．The result indicate that the reconstruct error is less than 0.4nT,average error is less than 0.1nT,error precision is between 0.1-0.5nT，achieve the requirement of geomagnetic relative instrument and the correlation coefficient between reconstruct signal and original signal is above 0.99．