Calcium ion, as an essential component in CASH, affects the aggregation and formation process of CASH, thereby influencing its microstructure and mechanical properties. However, the mechanism by which calcium ions affect the polymerization process of CASH is not yet fully understood. In this study, the effects of calcium ions on the polymerization process, coagulation state, and microstructure of CASH are investigated via molecular dynamics simulation. The results indicate that the presence of a trace amount of Ca²⁺ attracts oligomers towards the calcium-rich region, thus speeding up the polymerization to some extent, but as the Ca²⁺ content increases, more Ca²⁺ binds to the oxygen atoms in silica–oxygen tetrahedra and aluminum–oxygen tetrahedra, forming tight ion pairs and occupying the hydroxyl binding sites required for the polycondensation reaction. This inhibits the continuous aggregation of CASH gel and slows down the rate of polymerization. Additionally, Ca²⁺ attracts oxygen atoms from free water molecules and free OH⁻, forming Ca(OH)₂ dispersed in the spatial structure, which hinders the formation of larger clusters. As a result, the higher the Ca ion content in the system, the lower the overall polymerization degree of the CASH gel, resulting in a decrease in the conversion of the Q1 dimer to Q2 and Q3 chain structures, a shorter average chain length, poorer overall connectivity, and a transition from large clusters in a better-aggregated state to dispersed small clusters. This study sheds light on the polymerization reaction mechanism of CASH gels.