Abstract A thermoelectric system based on the interaction of composites of two metal nanocrystals in silica substrate prepared by a multilayer structure having alternate layers of metal/material mixture is discussed in detail in this paper. The alternate layers component of this work has two metal content, gold and silver. The layered structure irradiated with ionizing radiation to produce nanoclusters in these layers one on the top of each metal nanocrystal containing nanolayer with no silica buffer layer. The differing metal content serves to quench the nanoclusters to isolate nanoclusters along the 5.0 MeV Si beam irradiation track, as described in our past 16 years publications [1] , [2] , [3] , [4] , [5] . The result is a thermoelectric material with high electrical conductivity, low thermal conductivity, high Seebeck coefficient thus a high figure of merit as high as 3.1, as described in this work.