This research aims to investigate the synergistic reinforcing mechanisms of chemically combined graphene oxide and nanosilica (GO-NS) in the structure of calcium silicate hydrate (C-S-H) gels compared with physically combined GO/NS. The results confirmed that the NS chemically deposited on the GO surface formed a coating to keep GO from aggregation, while the connection between GO and NS in GO/NS was too weak to prevent GO from clumping, making GO-NS better dispersed than GO/NS in pore solution. When applied to cement composites, the incorporation of GO-NS enhanced the compressive strength by 27.3% after 1-day hydration compared to that of the plain sample. This is because that GO-NS generated multiple nucleation sites at early hydration, reduced the orientation index of calcium hydroxide (CH), and increased the polymerization degree of C-S-H gels. GO-NS acted as the platforms for the growing process of C-S-H, enhancing its interface bonding strength with C-S-H and increasing the connection degree of the silica chain. Furthermore, the well-dispersed GO-NS was prone to insert in C-S-H and induced deeper cross-linking, thereby refining the microstructure of C-S-H. All these effects on hydration products resulted in the mechanical improvement of cement.