The aim of this study is to improve the physical and mechanical properties of cement-based materials by adding nanometakaolinite clay (NKC). The results show the mechanism by which NKC modifies cement-based materials at the microscale level. A comparative experimental analysis of micromorphology and pore structure of cement specimens with NKC prepared using different NKC dispersion methods was performed to investigate the influence of the dispersion method and time on the dispersion of NKC in cement slurry. This showed that NKC can be efficiently dispersed in cement slurry by ultrasonic dispersion and stirring lasting 15 min, providing the most significant improvement to the cement pore structure. A large number of Ca(OH)2(CH) crystals in the early stage of hydration of cement are transformed into closely packed calcium silicate hydrate gel, thereby increasing the compactness of the cement matrix. After 28 days of standard curing, the CH crystal content in the hardened cements paste containing 5% of NKC by weight of cement was 12.72% lower than that of ordinary cement paste. The microscale analysis of the hardened cement paste showed that NKC can effectively fill the internal pores of cement-based materials, optimize the pore structure, and significantly improve the microscale compactness. NKC can also effectively improve the early mechanical properties of hardened cement paste. After curing for three days, the bending strength of cement paste prepared with 3% of NKC was 14.97% higher than that of ordinary cement paste. The compressive strength of hardened cement paste with 5% NKC addition was 15.13% higher than that of ordinary cement paste. During the ring test, the cracking time of cement mortar with NKC was earlier initiation and its surface stress–strain increased rapidly. Adding NKC increased the brittleness of hardened cement paste, which increased the risk of early age cracking.