With an optical microscope, transmission electron microscopic observation of naturally colored cotton fiber, its structure is similar to white cotton, but large cell and secondary cell wall thin, pigment are mainly distributed in secondary cell walls in fiber. Green cotton fiber coaxial osmium in the secondary cell wall layers, white cotton Brown cotton and there is no; green cotton coaxial osmium and wax, pigment related. Element analysis shows that only 85%~90% per cent of its fiber content; green cotton remaining components mainly for wax, content about 6~13 times that of white cotton. Colored cotton are approximately white cotton 1.4~1.6 ash content, protein content of about 1.75 per cent times the white cotton. Plasma spectroscopy shows that majority of colored cotton in trace metal content of less than white cotton, but copper and iron content above a white cotton.