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Graphite/epoxy resin (G/EP) composites are extensively utilized in bipolar plates for fuel cells owing to their outstanding electrical and mechanical properties. However, the mechanical strength of these composites declines notably due to the inadequate bonding interface between graphite and epoxy resin. To address this issue, we used molecular dynamics (MD) simulations to study the influence of graphite surface functionalization on the interfacial structures of composites. The results of this study revealed that the functionalization of the graphite surface led to an increase in the interface thickness of the composite. This phenomenon can be attributed to the interdiffusion and hydrogen bond formation between functionalized graphite and epoxy molecular chains. And all four types of functional groups demonstrated a promoting effect on the adsorption process. Additionally, the adsorption and contact angle results provided further evidence that the adsorption rate of graphite to the epoxy resin significantly improved after functionalization. These findings contribute to a more comprehensive understanding of the microscopic process of forming interfaces in G/EP composites. In addition, these insights provide valuable guidance for improving the interface bonding of composite bipolar plates, which can ultimately increase their mechanical strength.