A novel micro combustor embedded with high thermal conductivity material has been proposed for micro-thermophotovoltaic system application. The effect of the materials, which is graphite and nickel with widths 1 mm and 3 mm on the thermal and radiant performance of the new micro combustor, was experimentally and numerically investigated. It was found that high and uniform temperature distribution along the walls of the combustor was obtained by embedding graphite with width of 1 mm because of the enhanced heat transfer, which is desirable for the micro-thermophotovoltaic system. The available radiation energy increased from 4.6 W for the conventional combustor to 5.2 W for the novel combustor when the inlet velocity was 1.0 m/s and the hydrogen/oxygen equivalence ratio was 0.5 under the experimental conditions. The available radiation efficiency increased from 8.9% to 9.8% and the effect of the embedded material could be enhanced by increasing the chemical energy input. Based on the combustor and fuel in this study, the conditions for good thermal performance are graphite with width of 1 mm, inlet velocity of 1.0 m/s and 0.5 equivalence ratio of hydrogen/oxygen by considering the reliability and durability of the combustor.