Compared to ordinary Portland cement (OPC), sulphoaluminate/ferroaluminate cement (SAC/FAC) and aluminate cement (CAC) are the most promising repair materials due to their excellent early strengths, but the later strengths of SAC/FAC develop slowly, and the later strengths of CAC are obviously declined. This paper studied the effects of nano-SiO2 and nano-ZnO on the physical properties, mechanical properties, and early hydration processes of three special cement-based materials and compared them with OPC-based materials. The strength development and early hydration mechanism were revealed by hydration heat, scanning electron microscopy and X-ray diffraction. The test results showed that with the increasing content of nano-SiO2, the setting time of the four cement pastes was gradually shortened, the fluidity of four fresh mortars was gradually reduced, and their compressive and flexural strengths at all ages were improved to different degrees. Nano-ZnO significantly prolonged the setting time of OPC paste and increased the fluidity of OPC mortar, which had a negative effect on its early compressive and flexural strengths, but enhanced its late strengths. After the addition of 1% nano-ZnO, the initial time and final setting time of OPC were about 12 times and 13.4 times that of ordinary OPC paste, respectively. The effect of incorporating nano-ZnO on the physico-mechanical properties of three special cements was similar to that of nano-SiO2. The strength loss of CAC mortar with two kinds of nanoparticles was greatly reduced. The incorporation of nano-SiO2 and nano-ZnO could promote the hydration process of three special cements, resulting in the denser microstructure and higher crystallinity of hydration products.