A new process was proposed to control the defects in the ZMR-SOI thin film. Thermoelectric phenomena were adopted to the conventional lamp-ZMR. The effect of the new process was verified by the experimental examination and analyzed by the computer simulation. It was possible to control the defects by the ZMR with thermoelectric phenomena. The negative direct current density decreased the inter-defect spacing, while the positive current increased the defects spacing. It was shown by the computer simulation that the Peltier effect was the most dominant among the thermoelectric phenomena. The experimental results were correlated with the width of undercooling. A model was proposed to explain the mechanism of defect generation.