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In order to improve the spatial resolution of an optical micro-scanning thermal microscope system, the micro-scanning position must be accurately calibrated. An adaptive calibration method based on image registration and plane coordinate system is proposed. The meaning of calibration is given, and the principle and method of point calibration are introduced in detail and experiments using the real system were done. Different reconstruction methods were applied to reconstruct the visible light image and the real thermal microscope image, and the evaluation scores are given. Results of simulation and real thermal imaging processing show that the method can successfully calibrate the micro-scanning position. The method can significantly improve the oversampled reconstructed image quality, thus enhancing the spatial resolution of the system. This method can also be used in other electro-optical imaging systems.