The effects of different particle sizes(10,50nm) and content(0%, 1%, 3% and 5%) of nano SiO2(NS) on sulfate resistance of cement mortar under partial immersion were investigated. Before sulfate attack, the pore structure of NS blended mortar was analyzed. The mass loss ratio, linear expansion ratio as well as flexural and compressive strength loss ratio of attacked mortar were measured. The microtopography and phase composition of the immersed zone and drying zone of mortar were analyzed by SEM and XRD. The results show that NS can refine the internal pores of mortar and reduce the pore connectivity, enhance the sulfate resistance of cement mortar under partial immersion, and the enhancement increases with the increase of NS. Meanwhile, NS with particle size of 50 nm has better enhancement effect than NS with particle size of 10 nm. Ettringite and gypsum crystals are formed in the immersed zone and drying zone of mortar, but there is no thenardite crystallization in the drying zone, indicating that the main reason for the damage in this zone is chemical sulfate attack.