Graphene functionalization has been widely used in improving the thermal transport of graphene/epoxy composites owing to its performance in enhancing thermal conductivity and facilitating the formation of graphene networks. However, the heat transfer law and mechanism between functionalized graphene remain unclear. In this paper, the effects of distribution, type, and coverage of functional groups on the graphene−graphene interfacial thermal resistance (ITR) are analyzed by nonequilibrium molecular dynamics simulations. The results demonstrate that the graphene−graphene ITR depends on the synthetic effect of the graphene−graphene interaction, graphene−functional group interaction, and interaction between functional groups. The heat transfer contributions of those three interactions vary with the relative positions between functional groups. Then, the potential distribution of graphene is evaluated to compare the effects of different types of functional groups. It indicates that the potential difference is mainly attributed to functional groups. Compared with methyl, amino, and fluorine groups, hydroxyl groups have the largest potential difference and interaction. As the coverage of functional groups increases, the ITR of methylated graphene, aminated graphene, and hydroxylated graphene decreases inversely, whereas that of fluorinated graphene increases first and then decreases inversely. This work provides practical importance for the design and application of functionalized graphene in composite materials.