Abstract: Waterlogging significantly impacts agricultural production in the Huai River Basin. Revealing the spatial and temporal variation characteristics of waterlogging is crucial for disaster prevention and mitigation, as well as ensuring the safety of agricultural production. Meteorological data, including the daily precipitation (P), daily temperature (T), sunshine hours (SD) from 30 meteorological stations were selected to calculate the standardized precipitation evapotranspiration index (SPEI) from 1965 to 2016. The SPEI was employed to identify the intensity, frequency and area of waterlogging. Based on this, the temporal and spatial variation characteristics of waterlogging were analyzed. The results indicated that the annual SPEI in the Huai River Basin exhibited an increasing trend over the study period, with an increasing trend during spring, summer and autumn, whereas the SPEI in winter exhibited a declining trend. The annual waterlogging intensity reached a maximum of 21.32, primarily consisting of mild and moderate waterlogging. The affected area for each severity level showed a nonsignificant increasing trend. Seasonally, the highest waterlogging intensities were 17.64 in Spring, 51.72 in summer, 24.53 in autumn and 7.14 in winter. In spring, autumn, and winter, mild waterlogging events were predominant, with frequencies reaching 30.76%, 21.15% and 19.22%, respectively. The frequency of severe and above waterlogging was highest in summer, reaching 40.37%. The areas that were affected by waterlogging showed an increasing trend in all seasons except winter. These findings provide a certain scientific basis for disaster resistance and mitigation, as well as waterlogging risk prevention and control in the Huai River Basin.