Abstract: The working principle and application of X-ray energy dispersive spectrometer (EDS) in scanning electron microscope were briefly introduced. The common problems of spectral peak identification during the energy dispersive spectrometer analysis were false peaks and overlapping peaks. The identification methods of false peaks and overlapping peaks were emphatically introduced. The false peaks generally can be recognized by the instrument, and the overlapping peaks can be identified by following four methods:identifying by increasing the accelerating voltage and using multiple spectral lines, identifying by using the spectral reconstruction function and increasing the acquisition time, identifying by calculating the height ratio of actual peak and theoretical peak, and identifying by quantitative optimization method. Correctly identifying energy spectral peaks can improve the accuracy of qualitative and quantitative analysis of energy dispersive spectrometers.