UAV thermal infrared remote sensing technology, with its high flexibility and high temporal and spatial resolution, is crucial for understanding surface microthermal environments. Despite DJI Drones’ industry-leading position, the JPG format of their thermal images limits direct image stitching and further analysis, hindering their broad application. To address this, a format conversion system, ThermoSwitcher, was developed for DJI thermal JPG images, and this system was applied to surface microthermal environment analysis, taking two regions with various local zones in Nanjing as the research area. The results showed that ThermoSwitcher can quickly and losslessly convert thermal JPG images to the Geotiff format, which is further convenient for producing image mosaics and for local temperature extraction. The results also indicated significant heterogeneity in the study area’s temperature distribution, with high temperatures concentrated on sunlit artificial surfaces, and low temperatures corresponding to building shadows, dense vegetation, and water areas. The temperature distribution and change rates in different local zones were significantly influenced by surface cover type, material thermal properties, vegetation coverage, and building layout. Higher temperature change rates were observed in high-rise building and subway station areas, while lower rates were noted in water and vegetation-covered areas. Additionally, comparing the temperature distribution before and after image stitching revealed that the stitching process affected the temperature uniformity to some extent. The described format conversion system significantly enhances preprocessing efficiency, promoting advancements in drone remote sensing and refined surface microthermal environment research.