The thermal conductivity (TC) of graphene-based/metal composites is currently not satisfactory because of the existence of large interfacial thermal resistance between graphene and metal originating from the strong scattering of phonons. In this work, 6063Al-alloy-based reduced graphene oxide (rGO) composite with strong covalent bonds interface was prepared via self-assembly, reduction, and electrophoresis-deposition processes by using 3-aminopropyl triethoxysilane (APTS) as a link agent. Structural characterizations confirmed the successful construction of strong Al-O-Si-O-C covalent bonds in the as-prepared 6063Al-Ag-APTS-rGO composite, which can promote the transfer of phonons in the interface. Benefiting from the unique structure, 6063Al-Ag-APTS-rGO (214.1 W/mK) showed obviously higher cross-plane TC than 6063Al (195.6 W/mK). Comparative experiments showed that 6063Al-Ag-APTS-rGO has better cross-plane TC than 6063Al/Ag/ APTS/rGO (196.6 W/mK) prepared via physical mixing of stirring process, evidencing the significance of electrophoresisdeposition (EPD) process on constructing strong covalent bonds for improving the heat dissipation performance. Besides, the effects of different rGO contents and test temperature on the TC of the composites and their corrosion resistance were also discussed. This work demonstrated a feasible strategy for the construction of metal–carbon interface composite with improved thermal performance.