Alkali-activated materials (AAMs) offer significant benefits in the field of civil engineering, thanks to their energy-efficient and environmentally-friendly properties, as well as their exceptional strength and durability. However, the fundamental chemical reaction underlying the use of AAMs has not yet been fully understood. The process of the silicate depolymerization of the supplementary gelling materials is determined by their nano characteristics, which have certain restrictions by using experimental techniques. In this study, we utilized reactive molecular dynamics (MD) simulations to elucidate the chemical events occurring during alkali-activation in different AAMs. The sodium hydroxide (NaOH) solution selectively dissolves the silicon chains, while the aluminum chains remain intact. Furthermore, the laminar structures of silicon and aluminum in metakaolin (MK) crystal are entirely disturbed. However, the disintegration of silicon chains is negligible, and the Slag minerals maintain their layered structure. Calcium ions are crucial in stabilizing the chemical process of alkali activation. Furthermore, this study evaluates the fluctuations in their activity. Gaining insight into the minute details of this reaction provides essential theoretical foundations for developing eco-friendly and high-performing alkali-activated concrete materials.