<p>The optimal exploitation of geopolymers relies on a fundamental understanding of their atomic behavior, and molecular dynamics (MD) simulations provide a robust tool for addressing these issues. In this study, MD simulations are conducted to investigate the distinct behaviors of Ca²⁺ and Na⁺ ions during a&#xa0;geopolymer formation process. Simulation reveals that Na⁺ ions actively participate in polymerization, reacting with the silica-aluminum oxide precursor to form a sodium aluminosilicate hydrate (N–A–S–H) binder (geopolymer). As the Al content increases, more Na⁺ ions are involved in the chemical reaction. In contrast, the Ca²⁺ ions exhibit a&#xa0;different behavior, refraining from participating in polymerization and remaining suspended outside the geopolymer surface. The migration processes of Ca²⁺ and Na⁺ ions are thoroughly evaluated. Post-polymerization, molecular structure, and mechanical properties of the systems with varying Si/Al ratios are analyzed. The molecular structure analysis confirms the feasibility of this modeling method. Moreover, simulations of mechanical tests are conducted. Tensile test indicates that Na⁺ ions play a significant role in enhancing the mechanical strength. Shear test demonstrates the torsion and breakage characteristics of the atomic bonds. This study offers a perspective for addressing the conflict between the ease of breaking Al–O bonds and the existence of an optimal Si/Al ratio.</p> Graphical Abstract <p></p>