The invention discloses an optical coherence tomography method and an optical coherence tomography system for a complex polarization frequency domain. The method comprises the following steps of: on the basis of optical coherence tomography of a polarization frequency domain, driving a reference plane mirror of a reference arm to vibrate by a phase modulation device, introducing sinusoidal phase modulation while transversely scanning a sample, performing processing such as Fourier transform on acquired interference signals of horizontal and vertical polarization channels to obtain chromatography signals of the horizontal and vertical polarization channels without parasitic images, extracting magnitudes and phases of the chromatography signals respectively, and calculating to obtain an intensity image, a fast axis image and a delay image of the sample with double refraction properties within a full-depth range. According to the method, the imaging speed is high, a complex conjugate mirror image, a direct-current background and the self-coherence noise in the coherent tomography of the polarization frequency domain are removed, the sensitivity cannot be reduced along with the prolonging of a transverse scanning distance, and the method is not sensitive to motion blur in the sample.