To ascertain the inner structure diversity of the two different size sea pearls, some sea pearls including south pearls of China and south sea pearls were non-destructively analyzed by a new swept-source optical coherence tomography (OCT) technique and Raman spectroscopy. The Raman spectrum analysis results indicate that the phases of the nacre of all sea pearls are aragonite. Any artificial organic dye and additive were not found. The nacre thicknesses were speedily and effectively determinated based on the measuring function and graph manipulation function of this OCT technique. On the basis of the nacre thickness data, these sea pearls can be classified into five grades. The thickness and the diameter of the pearls were comparatively studied. The thicknesses of most of sea pearls have weak positive correlation with the diameters except several ones. In addition, according to the texture characteristics of OCT 2D images, the quality uniformity of nacre, transition layer and nucleus were classified and evaluated. The OCT technique could provide significant evidence for grade classification for nacre thickness and quality uniformity of pearls.