In this paper, molecular dynamics simulations are used to study the effects of temperature on the transport of chloride and sulfate in the nanopores of aluminum-doped cement-based materials (i.e., CASH gels) exposed to aqueous solutions of NaCl and Na₂SO₄ at 283, 293, 303, 333, and 363 K. It is shown that high temperatures increase the initial transport rates of water molecules and ions while weakening the hydration layer around ions. This increases the probability of ion–ion and ion–substrate contact and thus makes ions more likely to cluster in solution and be captured by the substrate. Both cluster formation and substrate capture can significantly restrict the free movement of ions in solution and thus gradually reduce the ion transport rate. In addition, since sulfate ions have four oxygen atoms that can capture other ions, large ion clusters form more readily in Na₂SO₄ solution than in NaCl solution. The capture of these large ion clusters at the interface can cause a “necking” phenomenon that hinders the subsequent transport of water molecules and ions into the nanopore. These results provide a nanoscale basis for designing aluminum-doped cement-based materials with enhanced durability at high temperatures.