Although its concentration is extremely low (about 5% of the volume of nacre) and its research technique is limited, the organic matrix in nacre not only is the most fundamental difference between biominerals and natural inorganic minerals but also has an important effect on biomineralization. In this study, the nacres of pearls and shells cultured in freshwaters and seawaters in Guangxi, Guangdong, Zhejiang and Jiangsu and those in corals were tested by Hitachi 835-50 High speed Amino Acid Analyzer and, as a result, the sorts and content of amino acids of organic matrix in nacre specimens were acquired. In combination with the microtopograpgy of nacre's organics investigated by SEM and HRTEM, the correlation analysis and cluster analysis produced some special amino acid constitutions or categories, which correspond to different organic macromolecules in different spatial positions, structures, kinds, shapes or sizes of nacres. These analyses show that the mineralization effect of organic matrix in nacre is characterized by diversity and complexity, which results in the diversity and complexity of inorganic minerals in species, size, evolution. Hence the unique microstructure of nacre can be formed by inducing and controlling. The conclusion obtained by the authors is significant for understanding the effect of organic matrix on biomineralization in nacre.