In order to make the thermal infrared remote sensing diagnosis of soil moisture content more accurate and efficient, different water treatments of field corn were taken as the research object, the plant and soil separation of thermal infrared image was realized by the visible light image of UAV and corn canopy temperature and surface soil temperature were extracted. Optimization of temperature information by eliminating 1% of temperature pixels at both ends of the temperature histogram was made to calculate crop water stress index (CWSI), canopy relative temperature difference (CRTD) and surface relative temperature difference (SRTD). The sum of the above three indices led to a new indicator which can diagnose soil moisture content at different depths. The results showed that there were higher correlation between the corn canopy temperature which eliminated 1% of temperature pixels at both ends of the temperature histogram and the measured canopy temperature (R2 was increased from 0.823, 0.886, 0.899 and 0.876 to 0.906, 0.938, 0.944 and 0.922 of four tests), and there were also higher correlation between the soil temperature which eliminated the 1% temperature pixel at the front of the temperature histogram and the measured soil temperature (R2 was increased from 0.841 and 0.875 to 0.908 and 0.925 of two tests), which indicated that the temperature optimized by the histogram method was closer to the measured temperature. In the early stage of jointing, CWSI and WTCI had better soil moisture content in the diagnosis of 0~20cm, while the soil moisture content in the late stage of jointing, tasselingsilking and maturity was better than that of 0~40cm. Under half coverage, WTCI1 with canopy temperature information (CWSI, CRTD) and soil temperature information (SRTD) was more correlated with soil moisture (0~40cm: R2 was 0.500 and 0.821, which was higher than 0.463 and 0.748)). Under full coverage, WTCI2 with canopy relative temperature difference (CRTD) was more correlated with soil moisture (0~40cm: R2 was 0.809 and 0.729, which was higher than 0.721 and 0.656), it indicated that WTCI was a new indicator for better diagnosis of soil moisture content. The research result provided new methods and new ideas for accurate acquisition of crop canopy temperature and accurate diagnosis of soil moisture content.