Urged by the increasing power density of electronics, efficient heat dissipation by graphene-embedded polymer composites with high thermal conductivity (λ) has become a growing demand for addressing overheating issues. However, it is still challenging to achieve a λ over 20 W m−1 K−1 below 20 wt% loading. Herein, we report a highly thermally conductive polymer composite based on self-assembled construction of horizontally aligned graphene/silver (f-GE/Ag) heterostructure, which is fabricated by in-situ deposition of ultra-small Ag nanoparticles on functionalized graphene followed by stress-induced orientation process, consequently achieving efficient heat-transfer pathways with low interfacial thermal barriers. The resultant f-GE/Ag contributes to the composite with a high λ of 25.22 W m−1 K−1 at 15 wt% loading, giving an ultra-high λ enhancement over 12500 %. Additionally, the thermal management application of composites as thermal interface materials integrated with power LEDs is demonstrated. The finding raises the possibility for practical application of high-performance polymer composites in the thermal management of electronics.