The effect of different limestone powder fineness on the chloride ion migration coefficient of the cement paste was tested using the Rapid Chloride Migration (RCM) method. The changes in the phase composition and pore structure of the paste were studied using hydration kinetics analysis, XRD and pore structure analysis. The results showed that before the chloride ion erosion, the limestone powder mainly exhibited filling effect, microcrystalline nucleation effect, and chemical activity effect. It reacted with the hydration products of cement to form calcium aluminate carbonate, which improved the strength of the hardened paste. After chloride ion erosion, the diffraction peak of calcium aluminate carbonate weakened, and Friedel’s salt was formed. With the increase of the specific surface area of limestone powder, the chemical activity of the powder became more obvious, and the generation of Friedel’s salt increased, leading to stronger resistance to chloride ion penetration. Limestone powder can reduce the porosity of the hardened paste and optimize the pore structure. When the particle size of the powder increased from 800 to 5000 mesh, the total porosity of the hardened paste decreased from 20.7% to 14.7%, and the most probable pore size decreased from 450nm to 75nm. Limestone powder with a particle size larger than 1500 mesh can fully exert its activity and play a role in solidifying chloride ions, thus improving the resistance to chloride ion penetration of limestone powder cement-based materials.