Dispersion compensation for the data processing of the spectral domain optical coherence tomography (SD-OCT) system is an important way to improve the imaging quality of the system. A dispersion compensation method for spectral domain optical coherence tomography based on numerical polynomial fitting analysis is proposed in this paper. This method obtains the dispersion factor by fitting the phase of the interference signal and removes the dispersion mismatch terms, which can significantly improve the system axial resolution compared with non-dispersion compensation. The SD-OCT system is used to measure the axial resolution and signal-to-noise ratio (SNR) at different positions of the optical path difference, and the effectiveness and reliability of the method are verified by analyzing the axial resolution and the SNR of the system before and after the dispersion compensation technology. Finally, we found that the third-order dispersion compensation has a visible optimization effect within the imaging depth of ~1.5 mm.