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It is significant to investigate the calcium carbonate (CaCO3) precipitation mechanism during the carbon capture process; nevertheless, CaCO3 precipitation is not clearly understood yet. Understanding the carbonation mechanism at the atomic level can contribute to the mineralization capture and utilization of carbon dioxide, as well as the development of new cementitious materials with high-performance. There are many factors, such as temperature and CO2 concentration, that can influence the carbonation reaction. In order to achieve better carbonation efficiency, the reaction conditions of carbonation should be fully verified. Therefore, based on molecular dynamics simulations, this paper investigates the atomic-scale mechanism of carbonation. We investigate the effect of carbonation factors, including temperature and concentration, on the kinetics of carbonation (polymerization rate and activation energy), the early nucleation of calcium carbonate, etc. Then, we analyze the local stresses of atoms to reveal the driving force of early stage carbonate nucleation and the reasons for the evolution of polymerization rate and activation energy. Results show that the higher the calcium concentration or temperature, the higher the polymerization rate of calcium carbonate. In addition, the activation energies of the carbonation reaction increase with the decrease in calcium concentrations.