Provided is a micro-fluidic heating system, which comprises a micro-fluidic control element for providing a chamber, a flow path and a valve, and a main body for heating the inside of the chamber in contact with the micro-fluidic control element, wherein the micro-fluidic control element consists of an upper substrate for providing the chamber, the flow path and the valve, and a lower substrate as a thin film bonded to the upper substrate, and the main body consists of a membrane in which heating means and suction holes are formed, and support member for supporting the membrane, and the heating means is partially in contact with the lower substrate of the chamber to heat the inside of the chamber, so that thermal transfer efficiency becomes maximized and temperature of each chamber may be independently controlled in the case of configuration having chambers arranged in array.