Cooperativity between pepsin and crystallization of calcium carbonate in distilled water was studied. The results show that vaterite was formed under the influence of pepsin and the crystalline product was a composite of vaterite and pepsin. The component of this material was similar to that of nacre. At the same time, the crystallization of calcium carbonate had also an important effect on the secondary structure of the pepsin. The secondary structure of the pepsin was characterized through FT-IR technology. The result indicated that the pure pepsin is composed of 24.38% alpha-helices, 29.91% beta-sheets, 39.32% beta-turns and 6.49% random structures and the pepsin in the CaCO(3)-pepsin solution is composed of 2.09% alpha-helices, 93.304% beta-sheets, 4.592% beta-turns and 0.006% random structure. During the crystallization of the calcium carbonate from the pepsin solution, the secondary structure of the pepsin transformed. These results showed that there was cooperativity between the crystallization of vaterite and the pepsin. The cooperative mechanism is discussed.