The characteristics of calcification in biocomposite are studied by adopting the molecular-level approaches such as X-ray, NMR, Zeta potential and analysis of secondary structure of organic matrix. The compositional and conformational features of organic matrix have a great influence on the structural properties (crystallite size, surface charge, stability, binding state, and polymorphic change). On the other hand, in synthetic calcium salts, the noticeable properties are not shown. From these results, the organic matrix by controlling specific peptide blocks is another key point for understanding of manifold morphology and superior biocomposite properties.