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A new thermal management application of silicon-based thermoelectric (TE) cooler integrated with high power light emitting diode (LED) is investigated in present study. The silicon-based TE cooler herein is fabricated by MEMS fabrication technology and flip-chip assembly process that is used for high power LED cooling. An electrical-thermal conversion method is used to estimate the junction temperature of LED. Moreover, the integrating sphere is also used to measure the light efficiency of LED. The thermal images photographed by infrared camera demonstrated the cooling function of the silicon-based TE devices. The results also show that high power LED integrated with silicon-based thermoelectric cooler package can effectively reduce the thermal resistance to zero. In addition, the light efficiency of the LED (1 W) will increase under low TE cooler input power (0.55 W), which is about 1.3 times of that without TE cooler packaging.