Sodium-containing calcium-alumino-silicate-hydrate (CNASH) gels, the primary binder phase of alkali-activated materials (AAMs), significantly impact the performance of the AAM. Although the effect of the calcium content on the AAM has been extensively studied in the past, few studies focus on the effect of calcium on the structure and performance of gels at a molecular scale. As an important element in gels, the effect of calcium in gels on its atomic-scale properties remains unclear. This study establishes a molecular model of the CNASH gel via reactive molecular dynamics (MD) simulation and verifies the feasibility of the gel model. By employing the reactive MD, the effect of calcium on the physicochemical properties of gels in the AAM is investigated. The simulation highlights that the condensation process of the system containing Ca is accelerated dramatically. This phenomenon is explained from the perspective of thermodynamics and kinetics. The increased calcium content enhances the thermodynamic stability and reduces the energy barrier of the reaction. Then, the phenomenon is further analyzed through the nanosegregation in the structure. It is proved that this behavior is driven by the weaker affinity of calcium for aluminosilicate chains than the particles in the aqueous environment. The difference in affinity leads to nanosegregation in the structure, making Si(OH)4 and Al(OH)3 monomers and oligomers closer for better polymerization.