We demonstrated a method for measurement of central corneal thickness (CCT) with a sub-micrometer sensitivity using a spectral domain optical coherence tomography system without needing a super broad bandwidth light source. By combining the frequency and phase components of Fourier transform, the method is capable of measurement of a large dynamic range with a high sensitivity. Absolute phases are retrieved by comparing the correlations between the detected and simulated interference fringes. The phase unwrapping ability of the present method was quantitatively tested by measuring the displacement of a piezo linear stage. The human CCTs of six volunteers were measured to verify its clinical application. It provides a potential tool for clinical diagnosis and research applications in ophthalmology.