This study investigates waterlogging disasters in winter wheat using the Agricultural Production Systems Simulator (APSIM) model. This research explores the effects of soil hypoxia on wheat root systems and the tolerance of wheat at different growth stages to waterlogging, proposing a model to quantify the degree of waterlogging in wheat. Remote sensing data on soil moisture and wheat distribution are utilized to establish a monitoring system for waterlogging disasters specific to winter wheat. The analysis focused on affected areas in Bengbu and Jingzhou. Experimental results from 2017 to 2022 indicate that the predominant levels of waterlogging disasters in Bengbu and Jingzhou were moderate and mild, with the proportion of mild waterlogging ranging from 30.1% to 39.3% and moderate waterlogging from 14.8% to 25.6%. A combined analysis of multi-source remote sensing data reveals the key roles of precipitation, evapotranspiration, and altitude in waterlogging disasters. This study highlights regional disparities in the distribution of waterlogging disaster risks, providing new strategies and tools for precise assessment of waterlogging disasters.