Calcium silicate hydrate (C-S-H) is the main hydration product of cement and the most important binder that plays a pivotal role in the mechanical properties of concrete. However, one of the major drawbacks of C-S-H is its high brittleness and low flexural strength due to its disordered structure at the nano- and micro-scales. Therefore, this study adopts graphene oxide (GO) to modify the structure of C-S-H, and investigates the effects of synthetic methods on the structure of C-S-H-GO composites. In this study, the highly ordered C-S-H-GO composite is successfully synthesized and exhibits itself the high toughness. Moreover, the formation mechanism of the highly ordered C-S-H-GO composite is explored and discussed, which provides a new insight into the design of high-toughness cement-based materials.