Amine-terminated macromolecular chain (ATBN) were covalently grafted on expanded graphite (EG) surface using 4,4′-methylene diphenyl diisocyanate as coupling agent. The functionalization result of the amine-terminated EG (AEG) was demonstrated by various analysis techniques. The AEG was incorporated into the epoxy (EP) matrix to form EP/AEG nanocomposites by interlayer polymerization in the EG interval layers. The grafted ATBN chains on the AEG surfaces can not only enhance the interfacial adhesion of the filler and EP matrix, but can also act as hardener to react with the EP chains covalently to further toughen the fabricated EP nanocomposites. The thermal stability, thermal conductivity, thermos-mechanical, and rheological properties of the EP/AEG nanocomposites were comprehensively studied. The results showed that the novel-designed AEG can significantly enhance the thermal conductivity of the EP composites. Moreover, the as-designed composites show superior thermal stability and thermo-physical properties, making them potentially useful as thermal management materials in electronic devices.