The partial replacement of cement with supplementary cementitious materials such as limestone powder can effectively reduce carbon emissions in the field of construction materials. However, its impact on durability still needs further exploration. The effects of limestone powder content, raw material fineness and water/binder ratio on chloride ion transport of cement-based materials were investigated by testing compressive strength, natural immersion of chloride ion and electromigration acceleration chloride ion transport. According to the phase composition and pore structure characteristics, the effect of limestone powder on the microstructure of system was studied. Combined with the macroscopic properties and microscopic analysis results, the relationship between chloride ion transport resistance and phase composition, pore tortuosity and critical pore size of system was discussed. The results show that in cement-limestone powder system, when the content of limestone powder is less than 15% (mass fraction), the influence of limestone powder on chloride ion transport resistance of system is small, and the formation factors can effectively measure the chloride ion transport resistance of system. In addition, the phase composition and pore tortuosity exhibit little correlation with chloride ion transport, and the critical pore size is the most important factor affecting chloride ion transport.