The unsaturated transport of water and ions in concrete structures accelerates the corrosion of reinforcing steel bars. Unfortunately, previous macroscopic and microscopic experimental studies have provided little clarity on the transport mechanisms of ions in calcium-silicate-hydrate (C-S-H) gels. This paper presents molecular dynamics simulations performed to investigate the effect of ion species and concentration during unsaturated transport processes. The transport rate of NaCl solutions at any given concentration significantly exceeds that of CaCl2 solutions because of desorption of intralayer calcium ions in the substrate. Additionally, the electric double layer effect of the realistic C-S-H gel substrate is more pronounced in NaCl solution than in CaCl2 solution and becomes stronger as the concentration increases in both cases. These insights into the effects of ion species and concentration on unsaturated ion transport and adsorption in realistic C-S-H gel nanopores will help guide the development of cement-based materials with improved corrosion resistance.