In order to prepare calcium carbonate nanoparticles in a green and environmentally friendly way, the concept of bio-mineralization has been proposed. Glucose, as a common small molecular organic substance found in organisms, participates in the mineralization process in cells. By adding glucose as a chemical additive, long chains of calcium carbonate form at the initial stage and then break granularly via over-carbonation. The average size of the calcium carbonate nanoparticles is about 40 nm based on the statistical analyses of three hundred particles. The growth mechanism of calcium carbonate under the influence of glucose is obtained. After the calcium carbonate nanoparticles are modified by sodium stearate, they are introduced to the PDMS matrix to achieve the composite material. Compared with pure PDMS, the composite with additional 3% calcium carbonate has its elongation at break and tensile strength increased by 23.96% and 48.15%, respectively.