The thermal microscope imaging technology can obtain non-contact imaging for fine target objects according to temperature changes, which is an important research direction in the field of photoelectric imaging technology. Due to the limited accuracy of the processing technology at present, the scanning position error will occur during the operation of the optical micro-scanning thermal microscope imaging system developed in the early stage. It will have a certain effect on the subsequent image embedding reconstruction, and the resolution of the reconstructed image is decreased. To solve the problem, a method of micro-scanning error correction by combining image pre-processing thought, micro-scanning principles, and calculating pixel-correlation is proposed. The results of simulation and experiment show that this method can improve the quality of image reconstruction and the spatial resolution of the system. The method can be directly applied to other photoelectric imaging systems to improve its performance.