There are intrinsic phase errors in swept source optical coherence tomography (SS-OCT), which severely influences the functional imaging. To overcome this difficulty, a numerical correction method is presented in this paper to correct the phase artifacts due to wavenumber shift among the spectral interferograms, resulting from the random delay variance between the sampling trigger and the clock of the swept source laser. This correction method is based on the linear relationship of phase difference to the depth of the sample and the wavenumber shift. The detailed procedure to eliminate the phase artifacts is as follows. Firstly, we figure out the complex OCT signals through inverse Fourier transform of the initial interferograms. Then we fit the upper surface of the sample with the intensity information of the B-scan by setting a floating threshold. After that the wavenumber shifts of each A-line are determined by two steps with the phase information of the sample surface: the relative wavenumber shifts between adjacent A-lines are first obtained according to the phase difference between the adjacent A-lines, the signal depth, and the linear relationship mentioned above; then we figure out the absolute wavenumber shifts between each A-line and the first A-line of the B-scan by an iteration algorithm. With the information about the wavenumber shift, we align the initial interferograms, and obtain the corrected complex signal through re-inverse Fourier transform of the aligned interferograms. This method introduces no extra noise, realizing phase measurement limited by the signal-to-noise ratio. It is noted that we take the average phase information of several axial pixels near the sample surface to diminish the noise influence when calculating the wavenumber shifts. Besides, this corrected algorithm acquires oversampling along the scanning direction to ensure the signal correlation between adjacent A-lines. The SS-OCT system in the paper is set up with a vertical cavity surface emitting laser with a center wavelength of 1297 nm. The system measurement range is 12 mm in lateral direction, the axial resolution is 17 m, and the lateral resolution is 24 m. And the feasibility of this method is verified by Doppler imaging of a mirror, an infra-red detection card and the cerebral cortex of a mouse.