At present, high-performance cement-based composites are widely used, and they are prone to early cracking due to their high autogenous shrinkage stress. In this research, the uniformly dispersed GNPs were added into high-performance cementitious materials. The autogenous shrinkage of high-performance cementitious matrix materials with different incorporation of GNPs was also researched with water to cement ratio of 0.25, 0.30 and 0.35. According to hydration heat, hydration products, microstructure and porosity of GNPs cementitious matrix materials, the microcosmic mechanism for autogenous shrinkage was also investigated. It was testified that moderate addition of GNPs decreased the autogenous shrinkage of cement-based composites. Moreover, the autogenous shrinkage value was minimal after treatment with 0.10 wt% GNPs cement paste sample for 7 days, at the water to cement ratio of 0.35, and the depressed percentage of autogenous shrinkage reached 81.60% compared with the blank sample.