The mutual inhibition effect of transport of sulphate and chloride in concrete specimen was determined in a macroscopic experiment. Higher concentration of sulphate has a better inhibition effect on chloride transport and the opposite is also true. In this paper, molecular dynamics (MD) simulation was performed to explore the effect of concentration (0, 0.5, 1.0 mol/L) on the transport of mixed solutions (NaCl and Na2SO4) in the main hydration products of aluminium-doped cement-based materials (i.e., calcium-aluminium-silicate-hydrate (C-A-S-H) gel). Sulphate was found to promote the aggregation of other ions to form ion clusters, which can reduce the effective width of the channel entrance and create a “necking” effect, thus reducing the overall transport rate of the solution. With the increase of NaCl concentration, sulphate ions in the mixed solution can adsorb more Na+ and Cl+ ions, and then form larger ion clusters to block the nanopores. Moreover, with increasing Na2SO4 concentration, higher amount of sulphate ions existing in the solution makes it possible to form more ion clusters. The results can provide a reasonable nanoscale explanation for macroscopic experiment.