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The application of microbial mineralization in cement-based materials has broad prospects, especially in strengthening the surface layer, improving the microstructure, and healing the cracks. This paper mainly studies the interaction between the mineralizing process by Bacillus mucilaginosus fixing CO2 from air and the hydration process of cement-based materials after addition of microorganisms. The coupling model described the interaction of the hydration of C3S and the microbial mineralization is established. This model is used to predict the contents of hydration products, the microbe induced bio-CaCO3 and the porosity distribution in hardened pastes of C3S. The calculated results revealed that the hydration degree of C3S, the contents of C-S-H gel and bio-CaCO3 increased and the remained C3S, the content of Ca(OH)2, the porosity decreased in certain depth of the surface layer of the hardened pastes of C3S after the addition of microorganisms. Moreover, the calculated results are in good agreement with the experimental.