With the developments in nanotechnology, the elaborate regulation of microstructure shows attractive potential in the design of new composite materials. Herein, composite materials composed of graphene network filled with metal nanoparticles are analyzed to optimize the fabrication process and mechanical properties. In the present work, molecular dynamic simulations are used to analyze the possibility of obtaining a composite structure with Ni-decorated graphene. The weak bonding at the graphene–copper and graphene–aluminum interfaces is manipulated by functionalizing graphene with nickel nanoclusters. It is found that Ni decoration considerably increases interfacial bonding and, at the same time, prevents the formation of a strong graphene network. It is found that Ni decoration for the Al/graphene composite increases the its ductility by 0.6, while increasing it for the Cu/graphene composite by about 0.5. Ultimate tensile strength of the composite with Al and Cu is close and equal to 22 GPa, respectively. The strength of the composite with Ni-decorated graphene is much lower and equal to 13 GPa for Cu/graphene/Ni and 17 GPa for Al/graphene/Ni. While Young’s modulus for the Cu/graphene composite is 18 GPA, for Al/graphene, Al/graphene/Ni, and Cu/graphene/Ni, it is 12 GPa. The obtained results demonstrate the future prospects of the graphene modification for better composite enhancement.