This Article is concerned with the interfacial thermal resistance for polymer composites reinforced by various covalently functionalized graphene. By using molecular dynamics simulations, the obtained results show that the covalent functionalization in graphene plays a significant role in reducing the graphene–paraffin interfacial thermal resistance. This reduction is dependent on the coverage and type of functional groups. Among the various functional groups, butyl is found to be the most effective one in reducing the interfacial thermal resistance, followed by methyl, phenyl, and formyl. The other functional groups under consideration such as carboxyl, hydroxyl, and amines are found to produce negligible reduction in the interfacial thermal resistance. For multilayer graphene with a layer number up to four, the interfacial thermal resistance is insensitive to the layer number. The effects of the different functional groups and the layer number on the interfacial thermal resistance are also elaborated using the vibrational density of states of the graphene and the paraffin matrix. The present findings provide useful guidelines in the application of functionalized graphene for practical thermal management.