This paper systematically studied the modification of cement-based materials by nano-SiO2 particles with an average diameter of about 20 nm. In order to obtain the effect of nano-SiO2 particles on the mechanical properties, hydration, and pore structure of cement-based materials, adding 1%, 3%, and 5% content of nano-SiO2 in cement paste, respectively. The results showed that the reaction of nano-SiO2 particles with Ca(OH)2 (crystal powder) started within 1 h, and formed C–S–H gel. The reaction speed was faster after aging for three days. The mechanical properties of cement-based materials were improved with the addition of 3% nano-SiO2, and the early strength enhancement of test pieces was obvious. Three-day compressive strength increased 33.2%, and 28-day compressive strength increased 18.5%. The exothermic peak of hydration heat of cement increased significantly after the addition of nano-SiO2. Appearance time of the exothermic peak was advanced and the total heat release increased. Thermogravimetric-differential scanning calorimetry (TG-DSC) analysis showed that nano-SiO2 promoted the formation of C–S–H gel. The results of mercury intrusion porosimetry (MIP) showed that the total porosity of cement paste with 3% nano-SiO2 was reduced by 5.51% and 5.4% at three days and 28 days, respectively, compared with the pure cement paste. At the same time, the pore structure of cement paste was optimized, and much-detrimental pores and detrimental pores decreased, while less harmful pores and innocuous pores increased.