Based on the observed daily runoff data from 7 hydrological stations covering 1960 to 2012 in the Lake Poyang Basin, this study identified and analyzed the spatiotemporal variations of the drought-flood abrupt alternation events (DFAAE) by applying the short drought-flood abrupt alternation index (SDFI), TFPW-MK trend test and Ensemble Empirical Mode Decomposition (EEMD). Further, the uncertainty of SDFI and the causes of DFAAE were also explored. The results revealed that DFAAE in Lake Poyang Basin generally occurred during March and October. Among these, the drought-to-flood events of Lake Poyang Basin mainly occurred during March and June, while the flood-to-drought events mainly occurred during July and October, with spatiotemporal difference existed between different ages. Mild DFAAE was the dominated events in the Lake Poyang Basin, while extreme DFAAE occurred less frequently. The extreme DFAAE was mainly concentrated in Fuhe River, Xinjiang River, and Raohe River sub-basins. Most of them were flood-to-drought events. The occurrence frequency of DFAAE was the highest in the 1990s and the lowest in 2000s. The TFPW-MK trend test of the minimum and maximum values of SDFI indicated there was a long-term decreasing trend in the intensity of the strongest flood-to-drought events of in the catchment except for Raohe River. Meanwhile, a decreasing trend for the occurrence intensity of the strongest drought-to-flood events was also found in Ganjiang River and the northern Xiushui River Basins. Relatively, an increasing trend occurred in Raihe River and the southern Xiushui River Basins. SDFI in the Lake Poyang Basin had two cycles which were 1 year and 21-35 years. In addition, there was a 3-year cycle in the occurrence intensity of the strongest DFAAE. The temporal and spatial variations of DFAAE were affected by spatial heterogeneity of precipitation and the strong human activities, etc. This study facilitates us to further understand the mechanism and change patterns of the extreme drought and flood events in the Lake Poyang Basin under the background of climate change. It also provides an important scientific basis for flood control, drought relief and disaster reduction in the Lake Poyang Basin.