The macroscopic mechanical performance of functionalized graphene sheets (FGS) reinforced cement composite is strongly associated with the interfacial bonding performance between FGS and calcium silicate hydrate (CSH). Herein, the interfacial bonding performance of CSH gel incorporated FGS with different functional groups (-H, –NH, –CH, –OH and –COOH) at various coverage degrees was studied using molecular dynamics. The simulated results indicated that the interfacial bonding performance between FGS and CSH can be optimized through tuning the functional group. Our simulations also indicated that the interfacial adhesive strength increase with the coverage degrees of the functionalized group. The GCOOH sheet, the GOH sheet and the GNH sheet can effectively increase the interfacial bonding strength of the composite due to these strong interactions with the CSH gel, but the addition of GCH sheet, GH sheet and pristine graphene sheet cannot. Subsequently, the static molecular structure, the dynamic properties and the mechanical interlocking effect were analyzed to elucidate the underlying mechanism of the discrepancy of interfacial bonding properties for different FGS/CSH composites. Our study explains the enhanced mechanism for the CSH gel incorporated various FGS at molecular level, providing a basis for the optimal design of cement-based materials using nanotechnology.