In order to improve the spatial resolution of the designed optical plate rotating micro-scanning thermal microscope imaging system, a method of optical micro-scanning super-resolution reconstruction for the thermal microscope imaging system was presented based on the improved frequency-domain image registration techniques and the new row action iterative method. The working principle and the method were analyzed. Different reconstruction methods were applied to reconstruct the visible image and the infrared image. Moreover, the evaluation parameters were given. Results of simulation and real thermal microscope images processing showed the availability of the method. The image spatial resolution and quality were improved with more detail. The system can be applied into many systems which need high spatial resolution minute thermal analysis. The algorithm can also be applied into the uncontrolled optical micro-scanning imaging systems and has wide application prospect.