The signification of discrete Fourier transform formulae with different coefficient is analyzed and the formula proper for engineering analysis is screened out. There are more ways to make the sample amount fit integral power of 2 for using fast Fourier transform. The strongpoint and the shortcoming of these ways is discussed. The applied objects of various frequency spectra are analyzed, the power spectral density is suitable for the noise of the electrostatically suspended accelerometer and the corresponding coefficient of window method should be selected. The correcting which must be used when the power spectral density is calculated by commercial software "Origin 5.0/7.0" of OriginLab Corporation is presented. The difference measurement of the noise of the electrostatically suspended accelerometers is required to bate the influence of environment noise in Ground. It is demonstrated that the differential method should be as follows: the noise of twin accelerometers in time domain, from which already deducted the average value, is subtracted mutually, whereafter is divided by sqrt{2}.