High thermal conductive filler (graphite flake) reinforced polymer composites have obtained a growing attention in the microelectronic industry. In order to overcome the obstacles in surface modification, in this study, dopamine chemistry was used to achieve the facile modification of graphite flake via forming a polydopamine (PDA) shell on the surface in a solvent-free aqueous condition. The strong pi-pi interaction between the hexagonal structural graphite flake and aromatic dopamine molecules ensured the effective modification. The PDA coating on graphite flake enhanced the compatibility between the filler and the flexible cycloaliphatic epoxy resin (CER) matrix via hydrogen bond, and promoted the epoxy curing process by forming covalent bond. Under the assistance of gravity, the PDA@graphite flake stacked along the horizontal direction in the polymer matrix. The procedure of filler alignment and mechanism of thermal decomposition were investigated by XRD measurement and thermodynamic/kinetics analysis, respectively. The dynamic mechanical analysis (DMA) was also used to investigate the relationship between microstructure and performance. Due to the combination of surface modification and alignment of PDA@graphite flake, the prepared CER/PDA@graphite has higher in-plane thermal conductivity. In addition, excellent adhesion property and thermal stability demonstrated that the CER/PDA@ graphite composites was a good candidate as thermal interface material (TIMs), which could be applied in the thermal management areas. The procedure was environment friendly, easy operation, and suitable for the practical application in large scale.