Carbonation plays an indispensable role in engineering construction, embracing mineralization, CO2 sequestration and low pH induced corrosion, but the essential mechanism of carbonation occurring in calcium silicate hydrate or portlandite can hardly be interpreted. Observation on how carbonation proceeds at the nano scale is thus critical for a better understanding of its dynamics. Here, using electron microscopy combined with first-principles calculation, a new view on carbonation in the cement system is revealed, considering morphological diversity, growth mechanism and shape evolution. Two types of crystalline forms of calcium carbonate (i.e. cubic and spindle) under room conditions were observed and determined to be calcite, both experimentally and theoretically. The mechanism of morphological evolution of calcite in a cement system was demonstrated based on the theory of aqueous chemistry. The [Ca2+] to [CO3] ratio was the principle cause for the diversity in crystal morphology instead of the types of reactants (i.e. portlandite or calcium silicate hydrates). Excess calcium species in the solution could selectively adsorb on surfaces, resulting in an inhibitive effect on the growth of specific crystal faces, (1 0 4)calcite and (2 1 1[combining macron])calcite in this case. Furthermore, a relationship between relative ionic concentration and the length to diameter ratio was established to predict the shape transformation. This work makes it possible to explore the chemical nature of carbonation from a nano scope rather than being confined to the macroscopic carbonation of concrete.