In this work, a new kind of double layers modified alumina-based hybrid ([email protected]@alumina ([email protected]@Al2O3) hybrid) was successfully synthesized through the two-step layer-by-layer process. First, copper (Cu) nanoparticles were assembled onto alumina (Al2O3) particles by reduction of Cu2+. Second, [email protected]@Al2O3 hybrids were assembled via Ag deposition on the surface of [email protected]2O3 particles. The obtained [email protected]@Al2O3 hybrids served as thermally conductive fillers to greatly boost the thermal conductivity of poly (dimethylsiloxane) (PDMS). The thermal conductivity reached 1.465 W m−1 K−1 at 85 wt% filler loading. The thermal conductivity of PDMS matrix was increased more than 7 times by the addition of [email protected]@Al2O3 hybrid, which was much higher than single layer modified alumina-based hybrids ([email protected]2O3 and [email protected]2O3 hybrids) and virgin Al2O3 particle. The effect of double layers modified filler, single layer modified filler and virgin filler on the thermal conductivity of PDMS matrix was discussed in detail and the mechanism of these fillers for improving thermal conductivity was studied through Foygel's thermal conduction model. Otherwise, electric, mechanical and thermal properties of [email protected]@Al2O3/PDMS composites were also further tested and analyzed.