Abstract: Abstract: Subsurface waterlogging is one of the primary agro-meteorological disasters threatening the wheat yield in the Middle and Lower Reaches of the Yangtze River. However, the current waterlogging assessment cannot fully meet the practical requirement in recent years, particularly without considering the hazard factors and the waterlogging tolerance variances in the growth period of the crop. In this study, a novel characteristic model was proposed using the Waterlogging Index (WI) index in the whole growth period, in order to represent the degree of wheat sub-surface waterlogging. Among them, the characteristic quantity (dimensionless parameter) was obtained to calculate from the APSIM (Agricultural Production Systems Simulator) model. After that, the influence of hypoxia on the total root system was evaluated to serve as the daily wheat waterlogging damage index. The average value on the daily influence function of wheat was taken to amplify 1 000 times for the WI index in the whole growth period. As such, the WI index was selected to consider the influence of soil hypoxia on the root system, and the variant of wheat waterlogging tolerance in the different growth stages, according to the daily soil volumetric water content. The relationship was finally determined between the spoilage index and wheat meteorological yield. The results show that: Meteorological yield was negatively correlated with the WI index (the complex correlation coefficient was 0.65, and the sample size was 14). Specifically, the higher the WI index was, the lower the meteorological yield was. The linear regression model was used to analyze the relationship between them. It was found that the regression curve intersected with the X-axis at 5.3 (i.e., the WI index greater than 5.3), while the meteorological yield was negative, indicating that the weather was unfavorable to wheat growth. Hench, WI of 5.3 was determined to be the threshold of spoilage. The soil moisture active passive (SMAP) soil surface moisture product data from 2016 to 2022 were substituted into the model, in order to calculate the WI index values of each grid point (10 km×10 km). The spatial distribution of the damage rate was obtained under the WI index greater than 5.3 as the damaged area. Specifically, the area was finally divided into the study area, according to the damage rate. The results showed that the wheat waterlogging areas in Hubei, Anhui, and Jiangsu provinces were concentrated along the Yangtze River, indicating the main risk area in the south of each province. The areas with the high risk of wheat waterlogging in Hunan and Jiangxi Province were distributed in the middle part of each province, whereas almost all the areas in Hunan and Jiangxi Province were in the middle-risk area. The total area of the no-waterlogging area accounted for 20.0%, whereas the low, medium, and high-risk area accounted for 14.8%, 30.1%, and 35.7%, respectively. This finding can also provide a new means for the spatial distribution of crop waterlogging risk assessment.