As the integrity of micro electronic devices improves, the heat power of chips is getting higher and higher. How to reduce the temperature of micro electronic devices effectively becomes more and more important. In this paper, a micro-channel cooler test system is set up. By measuring the temperature and pressure at inlet and outlet of the micro cooler and the average temperature of micro cooler bottom, the heat transfer performance of the copper based CNTs coated micro cooler is researched. The thermal resistance of copper and silicon based CNTs coated micro cooler are compared. It is shown that the copper based CNTs coated micro cooler has good thermal dissipation capacity than that of the Silicon based CNTs coated micro cooler.