Flexible nanocomposites incorporating nanofibrillated cellulose (NFC) hold significant promise for thermal management applications. However, their heat dissipation performance is primarily constrained by the interfacial thermal resistance (Rbd). In this work, 1-pyrenemethylamine hydrochloride (PyNH2) noncovalent functionalized graphene subsequently self-assembled with NFC through a vacuum-assisted filtration technique. PyNH2 could not only stabilize graphene with π-π conjugation but also interact with NFC via hydrogen bonding. The prepared layered-structure nanocomposites achieve a thermal conductivity of 11.32 W·m-1·K-1 with a low filler content of just 5 wt %. Utilizing the effective medium approximation (EMA) method and two-dimensional X-ray scattering techniques, we know that this satisfactory thermal conductivity is mainly attributed to pyrene functionalization of graphene by interfacial engineering-induced low Rbd and high orientation degree of graphene. Undoubtedly, this study provides experimental and theoretical guide for fabrication of thermal conductive nanocomposites in the near future.