A depth-dependent dispersion compensation method is presented to enhance the axial resolution in Fourier-domain optical coherence tomography. The dispersion compensation coefficients at different depths are calculated by an iterative algorithm, and a mathematical expression between the dispersion compensation coefficient and depth is obtained through numerical calculation. From the mathematical expression, the dispersion compensation coefficients at different depths are calculated to eliminate the high-order dispersion phase at different depths. The dispersion mismatch between the reference arm and sample arm is compensated and the broadening effect of dispersion is avoided. Theoretical derivation and experimental results in the optical coherence tomography systems show that the dispersion at different depths, including the deeper positions which have weaker signals, is effectively compensated by the depth-dependent dispersion compensation method and thus more structure informations of the sample are obtained.