Nano-C-S-H seed crystal, as an early strength agent for cement-based materials, has great application prospects. In order to investigate the effect of nano-C-S-H seed crystal on the early-age hydration process of Portland cement, in this article, low-field nuclear magnetic resonance (NMR) technology with 1H as a probe was used to in situ monitor the microstructure evolution of cement paste during the hydration process. Other micro-test methods including mercury intrusion porosimetry (MIP), scanning electron microscope (SEM), and X-ray diffraction (XRD) were also applied to characterize the microstructure of hardened cement paste. The results showed that nano-C-S-H seed crystal can promote the early hydration of cement, and the hydration promotion effect decreased with the hydration time and increased with the content of nano-C-S-H seed crystal. The average hydration rate of C-0.75 paste with addition of 0.75% nano-C-S-H seed crystal was the highest within 1 day of hydration, which was 7.75 times higher than that of pure cement C-0 paste. Nano-C-S-H seed crystal had a great effect on the pore size refinement of cement paste. After 7 days of hydration, the total porosity of all samples decreased to about 5%.