In the past few decades, the wetlands in the Nenjiang River basin have shrunk significantly, with serious soil salinization and frequent droughts, posing a severe threat to ecological security, water environment safety, and socio-economic sustainable development. Consequently, these issues have presented a serious challenge to the ecosystem in the Nenjiang River basin, resulting in a significant impact on the ecological balance. To gain a better understanding of the impacts of drought on ecosystems in the Nenjiang River Basin, this study analyzed the spatial and temporal evolution of ecological drought in the Nenjiang River Basin from 1980-2017 using the standardized ecological water deficit index (SEWDI) combined with the rotated empirical orthogonal function, cumulative sum, and Pearson correlation analysis, and extracted ecological drought characteristics using the runs theory. The findings revealed the following: Firstly, the correlation coefficients between ecological drought and the influencing factors ranked as relative humidity ＞ normalized difference vegetation index ＞ runoff ＞ precipitation ＞ temperature. The correlation coefficients of ecological drought and relative humidity were the largest and greater than 0.5, showing significant correlation, while the correlation coefficients of the rest of the factors were less than 0.5, showing a low degree of correlation. Secondly, from the change curve of the standardized ecological water deficit index, the alternation of wet and dry from 1980 to 1999 showed periodicity, and the ecological drought was dominated by mild and moderate drought, with a general trend of intensification; The extreme drought and extreme wet events occurred frequently from 2000 to 2017, but with an overall mitigating trend. The cumulative sum analysis revealed that 1980-1995 was the ecological normal fluctuation period of ecological dry and wet status in the Nenjiang River basin, 1996-2009 was the ecological dry period, and 2012-2017 was the ecological wet period. Thirdly, the drought duration, severity and intensity characteristics of ecological droughts show large differences in different spatial compartments. The ecological drought duration and intensity showed that the southwest part of the basin was more severe, with a higher risk of long-term drought, while the north part of the basin was more drought-intensive, and was more susceptible to a single, more severe short-term drought. Therefore, since different regions experience varying degrees of ecological impact from drought, it is necessary to tailor drought mitigation measures to the specific characteristics and needs of each region. Consequently, this approach will enhance the effectiveness of ecological system protection and ensure the sustainable development of the respective areas.