A comparative studies on the morphology of micro/nano-structure, the thickness of nacreous layer of natural-color golden seawater cultured pearl with different diameters and golden shades are carried out by ultra-violet and visible (UV-Vis) absorption spectrum, scanning electron microscopy (SEM) and high resolution transmission electronmicroscopy (HR-TEM). Furthermore, the relations between the thickness of nacreous layer and the color and the unique characteristic of UV-Vis spectra are further discussed. The results show that: the intensity of absorption band in UV-Vis absorption spectra is increasing as the deep color of golden-color pearl, the deep or light color of golden-color pearl has no direct relation with the thickness of nacreous layer. It is found that the thickness of nacreous layer located in different regions on the surface of golden-color pearl is different. Meanwhile, the density of “imbricate” structure and the morphology of the surface of golden-color pearl are different. The above characteristics maybe result to the slight varied UV-Vis absorption spectra with different regions on the surface of nacreous layer. In addition, one dimensional quasi-photonic bad gap structure exists in the nacreous layer of golden-color pearl, which should have close relations with the coloring of golden pearl and the density of golden-color.