The Huaihe River Basin (HRB), situated in the transitional area between northern and southern climate zones of China, is characterized by a complex geographical environment. Understanding flash droughts in the HRB is crucial for ensuring agricultural production. This study examines the spatial and temporal distribution characteristics and data uncertainty of flash droughts in the HRB from 2000 to 2020 using four sets of soil moisture data: ERA5, ERA5-LAND, GLDAS 2.1 and GLEAM 3.8a. The annual flash drought statistics show that the average occurrence count of flash droughts is generally higher in the ERA5 dataset, with a relatively uniform spatial distribution, while the results of the other three datasets exhibit a spatial distribution pattern of fewer occurrences in the north and more in the south. The average duration of flash droughts exhibits an approximately opposite distribution to their occurrence count distribution. The average occurrence count of flash droughts determines the spatial distribution of the occurrence frequency of flash droughts. Additionally, there is significant interannual variability in the occurrence count of flash droughts with considerable data uncertainty. Flash droughts in the HRB occur frequently during the crop growing seasons (April to September). Focusing on the crop growing seasons, the spatial distribution of the average occurrence count of flash droughts is similar to that of the annual results. However, the average duration of flash droughts tends to be shorter compared to the annual results. The southern region of the HRB experiences more flash droughts during the crop growing seasons, and their interannual trends also exhibit significant data uncertainty.