Abstract Although amino trimethylene phosphoric acid (ATMP) has been widely used as a retarder for Portland cement, its effect on cement hydration is poorly understood at the atomic level. In this study, we combine static calculation and ab initio molecular dynamics (AIMD) simulation to reveal the mechanism of the effect of ATMP on the initial stage of C 3 S hydration from multiple perspectives, quantitatively analyze the structural reconstruction and charge migration at the ATMP/C 3 S interface in the aqueous environment. By adsorbing on the surface of C 3 S, ATMP occupies the adsorption site of water molecules. Compared with the pure C 3 S surface, the addition of ATMP delays the hydroxylation of the C 3 S surface and inhibits the formation of Ca‐Ow bonds. This work gives new insights into understanding the hydration of C 3 S with ATMP and offers new approach of designing new cement retarder at the molecular level.