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This article contains data related to the research article entitled “Atomistic simulation on nanomechanical response of indented graphene/nickel system” (Yan et al., 2017). There are five sets of data obtained by molecular dynamics simulations for nanoindentation of five different graphene/nickel systems, which are single nickel system, monolayer graphene on nickel system, double-layer graphene on nickel system, three-layer graphene on nickel system and four-layer graphene on nickel system. The calculated load-displacement of the five different indented systems is also listed.