Ions that penetrate concrete micropores have a significant influence on concrete’s properties. Studying the microscopic interaction mechanisms between ions and concrete materials allows the discovery of factors that significantly affect concrete properties from a new perspective. In this study, molecular dynamics techniques were used to simulate the transport processes of different ionic compounds (Na₂SO₄, NaCl and NaNO₂) in C-S-H gel nanopores in a pairwise coupled way, so that a detailed investigation into how these ions interact with each other and how they affect C-S-H gel could be carried out. It was found that for anions entering the C-S-H gel nanopores, the order of transport rate is SO₄^2->Cl^->NO₂^–. Furthermore, the SO₄-Na ion pair greatly affects the transport rate of solution due to its strong binding stability. Additionally, this study found that the presence of sulfate ions changed the transport characteristics of nitrite ions, such that nitrite ions aggregated into clusters more easily, thereby disrupting the compatibility between nitrite ions and water molecules. As a result, the presence of sulfate ions reduced the rustproofing effect of nitrite ions.