The effect of different particle sizes (10 and 50nm) and content (0, 1%, 3% and 5%) of nano-SiO2 (NS) on sulfate attack on cement mortar under partially immersion was investigated. Before sulfate attack, the pore structure of NS blended mortar was analyzed. And then, the mass loss rate, linear expansion rate as well as flexural and compressive strength loss rate of attacked mortar were measured, and the microtopography and phase composition of the immersed and drying zones of mortar were analyzed by SEM and XRD. The results show that NS refined the internal pores of mortar and reduced the pore connectivity, thereby its incorporation enhanced the sulfate resistance of cement mortar under partially immersion, and the enhancement increased with the increase of NS. Meanwhile, NS with particle size of 50 nm had better enhancement effect than NS with particle size of 10 nm. Ettringite and gypsum crystals were formed in the immersed and drying zones of mortar, but there was no thenardite crystallization in the drying zone, indicating that the main reason for the damage in this zone was chemical sulfate attack.