The durability of cement-based materials is closely related to the transmission characteristics of water and chloride ions in the pores of calcium silicate hydrate (C-S-H) gel, especially in the climate conditions with significant temperature difference. The local structure and transport process of water molecules and chloride ions in gel pores are affected by interfacial effects. The unsaturated transport model of sodium chloride solution in C-S-H gel pores is established on the molecular scale, under different temperature and pore size conditions. Divide the regions in the C-S-H gel pore model into internal adsorption zone, external adsorption zone, and free zone. Taking into account the intrinsic mechanisms and molecular properties of water molecules and ions during transport in the C-S-H gel pores, the local structures and dynamic properties of water molecules and ions in the gel pores are quantitatively described. The electrical double layer and the double-layer water film overlap in the 1.5 nm gel pore, the water molecule and the chloride ion are closely arranged. Thus the diffusion coefficient is far lower than others, and is rarely affected by temperature. Considering the changes in the molecule properties of water and ion in different zones in molecular simulation results, a theoretical model of nanopore water and ion migration was established, revealing the migration behavior of water and ions. The results indicate that the steady-state diffusion fluxes of water and chloride ions are positively correlated with the effects of temperature and pore size, and the increasing amplitude of their diffusion fluxes is characterised by a similar phenomenon with that. This research provides a theoretical basis for the mechanism and durability of cement-based materials corroded by water and chloride ions in marine environments.