The rheometer was used to test the rheology of cement paste with and without nano-silica, and the fluidity and free water content were tested, the isothermal calorimetry of cement and C3S was tested and hydration products were monitored using Raman spectroscopy. A modified Bingham model was used to describe the rheological properties of the paste, and the effects of nano-silica with different particle sizes on rheological parameters including yield stress, plastic viscosity and thixotropy were derived. The results show that the fresh state properties of the cement paste vary with the particle size of nano-silica at the same dosage. The decrease in the particle size of nano-silica reduces the fluidity and free water content, but increases the yield stress and plastic viscosity. The flocculation and surface water absorption of nano-silica reduce the free water content at 5 minutes, which results in a decrease in flow diameter and an increase in yield stress. During the time evolution, the heat of hydration and Raman spectroscopy show that nano-silica with smaller particle size has higher nucleation and pozzolanic effect, that is, with the same dosage, nano-silica with small particle size provides more nucleation sites to form calcium silicate hydrate (C-S-H) seeds and to promote the hydration of C3S and the formation of C-S-H.