The prism layer is obviously different from the parallel layer in sea-cultured pearl. XRD, optical microscopy and micros-IR have been applied to the crystallized layers of good and poor quality sea-cultured pearls from South China. The result shows that the prism layer is not composed of calcite. There are three types of prism in sea cultured pearl: calcite prism, aragonite prism, calcite + aragonite prism. Therefore, we have a new understanding of the biomineralization characteristics of prism layer in sea-cultured pearl. The result makes us renew the traditional explanation that the content of aragonite affects the quality of pearl. Because some sea prism pearl is composed almost completely of aragonite, but the quality of this kind of pearl is worst. The thickness and spatial distribution of prisms are one of the main factors which affect the quality of sea cultured pearl.