A method of compensating dispersion precisely in Fourier domain optical coherence tomography was proposed, based on the combination of the measurements of the values of the dispersion with the rapid scanning optical delay line. Firstly, a plane mirror was placed in the sample arm, and the values of differences of the group delay dispersion were measured while moving the grating in rapid scanning optical delay line to introduce differentdispersion. When the measured value was zero, the dispersion was matched. The new method was compared with the one based on the full width at half maxmum of point spread function. It was found that the measuring error of full width at half maxmum was 4.43% while proposed method was 0.76% and the sensitivity of full width at half the maxmum decreased from 92.105 3 fs2 to 1.344 7×103 fs2 while it remained 165.789 5 fs2 in the proposed method. The results show that this method is more accurate and sensitive than the full width at half the maximum. In addition, the direction of grating movement can be determined by the sign of the measured value of dispersion difference, which may be used to compensate dispersion. Finally, the experimental data show that the axial resolution after compensating dispersion nearly approaches the theoretical value.