Waterlogging harms winter wheat growth. To enable accurate monitoring of agricultural waterlogging, this paper conducts a winter wheat waterlogging monitoring study using multi-source data in Guzhen County, Anhui Province, China. The hydrological model HYDRUS-1D is coupled with the crop growth model WOFOST, and the Ensemble Kalman Filter is used to assimilate Sentinel-1 inversion soil moisture data. According to the precision and continuity of soil moisture, the damage of winter wheat waterlogging were obtained. The experimental results show that the accuracy of the soil moisture is improved after data assimilation compared with that before data assimilation, and the Nash–Sutcliffe efficiency (NSE) of the simulated soil moisture values at three monitoring sites increased from 0.528, 0.541 and 0.575 to 0.752, 0.692 and 0.731, respectively. A new waterlogging identification criterion has been proposed based on the growth periods and probability distribution of soil moisture. The proportion, calculated from this identification criterion, of the waterlogging wheat farmland in total farmland shows a high correlation with the yield reduction rate. The correlation coefficient of the waterlogging farmland proportion and the yield reduction rate in 11 towns of Guzhen County reaches 0.78. Through the synchronization of geography, agriculture and meteorology, the framework shows great potential in waterlogging monitoring.