Ni–graphene nanocomposites with high-density interfaces have enormous potential as irradiation-tolerant materials applied in Gen-IV reactors. Nevertheless, the mechanism wherein the intrinsic and/or irradiation-induced defects of graphene affect the irradiation tolerance of the composites remains poorly understood. Here, we investigate the effects of the two types of defective graphene on the displacement damage and He diffusion of the composites, respectively, using atomistic simulations. The introduction of the intrinsic defects of graphene has a significant effect on the Ni lattice structure near the Ni–graphene interface, especially showing that after displacement cascades, the number of defects gradually increases with the increase in graphene-defective size due to the formation and growth of stacking fault tetrahedra. The existence of the irradiation-induced defects of graphene does not diminish the ability of the interface to trap He atoms/clusters and even may be maintained or improved, mainly reflected in the fact that many isolated He atoms and small clusters can gradually migrate toward the interface and the fraction of He within the interface is up to 37.72% after 1 ns. This study provides an important insight into the understanding of the association relationships of defective graphene with the irradiation tolerance of composites.