Thermoelectric cooler has been widely used in the thermal management of various electronic devices. However, the application of micro-thermoelectric cooler to high power light-emitting diode still needs to be further explored at present. This paper aims to establish a model of high power light-emitting diode package integrated with micro-thermoelectric cooler and explore the performance of this system under various interfacial and size effects. An experiment is conducted to validate the model. Five types of the micro-thermoelectric coolers are designed and integrated to the light-emitting diode package to reduce the localized junction temperature of the light-emitting diode chip. The influence of interfacial effects, thermoelectric element size, and driving power of micro-thermoelectric cooler on the system-level thermal and optical performance is discussed. Results indicate that the micro-thermoelectric cooler with 6 x 6 thermoelectric elements shows the best cooling performance for the driving power of micro-thermoelectric cooler lower than 0.85 W. For thermoelectric cooler with 6 x 6 thermoelectric elements, a minimum chip junction of 95.9 degrees C, which is 12.3 degrees C lower than that of the light emitting diode without micro-thermoelectric cooler, can be achieved. This characteristic can increase the luminous efficacy and lifetime by 12.3% and 50%, respectively. It also found that the electrical boundary resistance plays a more dominant role, compared with the thermal boundary resistance. However, the thermal contact resistance exhibits greater adverse impact than the electrical contact resistance. In addition, a total performance improvement proportion of 25.5% can still be achieved, although the micro-thermoelectric cooler consumes power energy by 22.5% at the driving power of 0.87 W.