In order to improve the accuracy of retrieving soil moisture content based on canopy temperature information, taking the different moisture treatment of the jointing field corn as the research object, and the UAV thermal infrared and visible light camera were used to obtain the remote sensing images of the experimental area. Different image classification methods were applied to remove the soil background and extract corn coverage and canopy temperature, then the indices such as crowntemperature difference and the ratio of crowntemperature to coverage were calculated, and the relationship between the two indices and soil moisture content was analyzed subsequently. The results showed that there were differences in corn coverage extracted by different classification methods, and there were also differences in corn canopy temperature extracted by different classification methods. The crowntemperature difference, crowntemperature difference to coverage ratio calculated by three classification methods (Grayscale segmentation, RGRI index, GBRI index) had a linear relationship with soil moisture content, and it was better to invert the soil moisture content of 0~30cm corn root depth by the two indices; the crowntemperature difference without removing the soil background held the worst effect on soil moisture content, while removing soil background by GBRI index classification enjoyed the better effect on the soil moisture content（R2 was improved from 0.255，0.360 and 0.131 to 0.425，0.538 and 0.258 at depth of 0~10cm，10~20cm and 20~30cm）; the ratio of crowntemperature difference to coverage inversion of soil moisture content performed much better than that of crowntemperature difference. At the depth of 0~10cm，10~20cm and 20~30cm, R2 was 0.488，0.600 and 0.290 in the model set, P<0.001, and R2 was 0.714，0.773 and 0.446 in the verification set, indicating that the ratio of crowntemperature difference to coverage was a new indicator for reversing the effect of deep soil moisture in the corn root zone. This study provided a new method for inversion of the soil moisture content of corn in the field by thermal infrared remote sensing.