The existing identification of wheat lodging based on unmanned aerial vehicle (UAV) is significantly dependent on the artificial ground annotation method, which exhibits low annotation accuracy and strong subjectivity, thus resulting in a low degree of separation for the annotated lodging area and the non-lodging area. To solve the problem of insufficient applicability of traditional annotation research to agricultural images, especially wheat field lodging images, a lodging annotation method in the study based on semi-automatic image segmentation algorithm was proposed. Firstly, a total of 101 farmlands with lodging occurred during the flowering, filling and mature period of wheat in 2019 and 2021 were segmented as the research objects. The above images were respectively changed into RGB and HSV color space and converted into four vegetation indexes, including excess-green (ExG), green leaf index (VEG), normalized green-red difference index (NGRDI), as well as red-green ratio index (GRRI). Secondly, lodging regions were extracted and modified from the image in accordance with color features. Lastly, the JM distance of lodging and non-lodging areas served as an index to examine the effect of image annotation for data analysis and evaluation of segmentation accuracy. The result of the experiment indicated that there was a very significant difference between the JM distance based on the annotation method proposed in this study and the result based on manual annotation. GRRI and ExG were the most suitable features for image annotation. The method proposed in this study had high generalization performance for the images captured in the three fertility periods in 2019 and 2021, and the images with poor image annotation results took up a small proportion. In brief, the lodging area annotation method proposed in this study increases the annotation accuracy by extracting lodging areas using a semi-automatic image segmentation algorithm. The proposed method outperforms the manual annotation method.