The combination of polymer and copper (Cu) is common and economical in thermal interface materials (TIMs). However, it is remains challenging for traditional polymer-Cu composites to obtain high thermal conductivity (TC) (>10 Wm−1K−1) due to the poor filler connection. Herein, we introduced small amount of 2D-structured graphite nanoplatelets (GNPs) into bulk Cu flakes/epoxy composites via the thermal molding method. Surprisingly, we found an extraordinary synergistic effect, revealed highly thermally conductive percolation network through intercalation of GNPs between Cu flakes. A high isotropic TC 13.4 Wm−1K−1 is achieved with 5 wt% GNPs and 80 wt% Cu flakes, which superior than most reported Cu/polymer composites. Although a high electrical conductivity of 34000 S/m was obtained, a phonon-dominated thermal transport mechanism was observed due to the existence of GNPs bridges between Cu flakes. The resulting composite also demonstrate excellent thermal management ability, superior acid resistance and good mechanical property, which offers a promising composite in thermal management application.