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This paper provides an intrinsic mechanism for alkali dissolution from the gels of geopolymers at the nanoscale, via a molecular dynamics (MD) investigation on N-A-S-H gel, the predominant binding phase in geopolymers. Sodium plays roles in balancing the charges of [AlO4] tetrahedrons, and its absence causes local structures to show a negative charge, resulting in locally mutual repulsion between tetrahedrons. Also, sodium dissociation promotes a hydrolytic reaction, exacerbating the non-conservation of charge of the N-A-S-H system, further swelling the structure. The above evolution weakens the alumino-silicate skeleton and reduces the stability of silicate and aluminate species, which in turn promotes sodium dissociation. In the long term, it increases the potential of structure depolymerization and even peeling off. Based on previously reported experiments and our computational results, it is likely that leaching starts from the N-A-S-H substrate surface, and the gel peels off layer by layer in the above manner, resulting in microscopic holes and fissures. In addition, leaching also leads to the degradation of the mechanical properties of the surface gel, including Young's modulus, tensile strength, and ductility, which considerably increases the possibility of surface gel peeling. Additionally, sodium is able to connect [AlO4] and [SiO4] tetrahedrons by the electrostatic force with tetrahedral oxygen, which transfers stress and contributes to uniform stress dispersion.