The dispersion compensation method based on frequency domain analysis (FDA) is proposed. The interference signal acquired from the optical coherence microscopy (OCM) is Fourier transformed to the frequency domain and the mean wavenumber corresponding to the peak frequency amplitude is obtained. A polynomial is fit to the unwrapped phase centered on the mean wavenumber in order to estimate the coefficient of the second order dispersion. In the experiment, dispersive elements with different thicknesses are inserted into the reference arm to calculate the second order dispersion coefficients corresponding to the optical path differences (OPDs) of the dispersive elements of two interference arms. A linear least squares fit demonstrates the good linearity between the second order dispersion coefficient and the relative thickness of the dispersive elements. In accordance with this linearity, a dispersive element with the appropriate thickness inserted into the reference arm will compensate the second order dispersion of the interference system.