The exquisite structure of natural materials manifests the importance of particle mobility and load transfer in developing advanced polymer nanocomposites; however, it is difficult to concurrently meet these two mutually exclusive requirements. To address this issue, we demonstrate an approach that constructs a hierarchical, flexible interphase structure in epoxy nanocomposites through a local amine-rich environment around graphene sheets (GNs) and volume exclusion effect of grafting chains. Long-chain aromatic amines, which are chemically similar to the curing agent, are covalently bonded on the surface of GNs by diazonium addition. They play multifold roles in the structure formation of epoxy composites, (1) promoting the exfoliation and molecular level dispersion of GNs in the matrix, (2) serving as a linker between GNs and epoxy networks for improved load transfer, (3) modulating the stoichiometric ratio around GNs to construct a hierarchical structure that can dissipate more strain energy during fracture. With the addition of 0.6 wt% amine-functionalized GNs, the resulting composite exhibits significant mechanical improvements, 93.8 and 91.5% increases in fracture toughness and flexural strength, respectively. This approach affords a novel design strategy for developing high-performance structural composites.