Living matters produce various materials in their bodies without consuming thermal energy. The natural bodies can be considered as material manufacturing plants with high-efficiency. In the biological synthesis of inorganic solids, an organism creates a proper organic matrix, and the crystals precipitate onto the matrix due to chemical interactions of an inorganic/organic hetero-interface. We attempted to apply this mechanism in material synthesis to produce nano-sized calcium phosphate crystals. Phase separated microenvironments of organic molecules were employed as microreactors for the nano crystals formation. Organic functional group bounded water mediated calcium phosphate crystal nucleation, and the nano-sized crystals were obtained.