Ecological drought is a complex process in terrestrial ecosystems where vegetation's eco-physiological functions are impaired due to water stress. However, there is currently a lack of long-term assessment of ecological drought from an eco-physiological perspective. In this study, the standardized ecological drought index (SESNDI) was developed using actual evaporation, root soil moisture, and kernel normalized difference vegetation index via the Euclidean distance method, reflecting ecosystem physiology, water supply capacity, and vegetation status. Solar-induced chlorophyll fluorescence validated SESNDI by reflecting vegetation photosynthesis. Using China as an example, severely impacted by climate change and ecological restoration, ecological drought's spatio-temporal variation and propagation characteristics was evaluated using clustering algorithms. The results demonstrated that (1) SESNDI showed superior performance over several other drought indices. (2) During 1982-2020, ecological drought was prevalent from 1990 to 2010, especially in the central and northeastern regions. (3) Compared to 1982-2000, the median duration and affected area of ecological drought events during 2001-2020 reduced by four months and 1.51 × 10 5 km 2 , respectively, while the median intensity increased by 0.06. (4) Decreased precipitation and increased temperature were the primary factors contributing to the frequent occurrence of ecological drought in China from 1990 to 2010. This study offers a crucial methodology for evaluating ecological drought, serving as a reference for developing effective terrestrial restoration strategies.