Alkali and alkali earth metal ions are normally present in the gels of alkali-activated materials as well as blended PC-based materials. Previous studies have revealed that the leaching of these cations can trigger the change in gel structure and even the gel decomposition. However, the dissolution of cations was rarely known and the underlying mechanisms remained unclear. To address this issue, five calcium-(sodium, potassium-)aluminum-silicate hydrates (C-(N,K-)A-S-H gels) with different Ca/Si ratios (0.8–1.2) and Al/Si ratios (0.1–0.3) were synthesized to investigate the leaching behaviour of Ca, Na and K. For the first time, the dissolution free energies of Ca, Na and K in C-(N,K-)A-S-H gels were calculated using molecular dynamics simulations with the metadynamics method. Experimental results showed that Na showed the highest leaching ratio, followed by K and Ca, attributed to the lowest dissolution free energy of Na. The gel with a higher Ca/Si ratio or a lower Al/Si ratio showed higher charge positivity on the surface, resulting in reduced leaching of the three cations. Additionally, the presence of K was found to promote the dissolution of Na in gels.