The present invention provides an apparatus and method for performing heat-exchanging reactions on an electro wetting-based micro fluidic device. The apparatus provides one or multiple thermal contacts to an electro wetting-based device, where each thermal contact controls the part of the electro wetting-based device it communicates with to a designed temperature. The electrowetting-based device can be used to create, merge and mix liquids in the format of droplets and transport them to different temperature zones on the micro fluidic device. The apparatus and methods of the invention can be used for heat-exchanging chemical processes such as polymerase chain reaction (PCR) and other DNA reactions, such as ligase chain reactions, for DNA amplification and synthesis, and for real-time PCR.