Regarding watershed as an indivisible organic whole with self-organizing capability, in order to characterize its ecological sustainability, the spatio-temporal information entropy method combining spatial information entropy and temporal information entropy was proposed from the perspective of entropy. The spatial information entropy was used to characterize the order degree of ecosystem pattern in spatial distribution, and the temporal information entropy was used to measure whether the dynamic evolution of ecosystem was orderly or not. The spatio-temporal information entropy method analyzed the sustainability of watershed ecosystem quantitatively by combining pattern and dynamics. Taking Yanhe watershed as the study area, based on three-period land use data and long time series Normalized Difference Vegetation Index (NDVI) data, the ecological sustainability of Yanhe watershed from 2000 to 2018 was analyzed using the spatio-temporal information entropy method. The results showed that: (1) the ecosystem pattern of the Yanhe watershed changed in an orderly direction, indicating that the Yanhe watershed was in the growth or recovery period as a whole. (2) The distribution of temporal information entropy showed the spatial heterogeneity. The temporal information entropy values in the south and southwest of the study area were the lowest, while the values of the north and central were higher, and the values in the northwest and southeast were the staggered distribution. The temporal information entropy values of the cultivated land, middle and low coverage grassland and other woodland were higher than others, so the ecological resilience of these vegetation types was stronger. The pattern of cultivated land with middle coverage grassland could be adopted in the future. (3) The ecological sustainability was mainly strong and less strong (totally 61%), most of which were distributed in the central and northern regions, indicating that the ecological resilience capacity of Yanhe watershed was mostly enhanced and the overall situation of ecological sustainability was significantly improved. The proportion of weak and less weak was the lowest (totally 13%), which was concentrated in the northwest and south ends of the basin, and the ecological sustainability of these regions still needed to be further improved. Specific ecological management measures were formulated for different grades of regions. This research is a useful exploration for the study of ecological sustainability from the perspective of entropy, which provides a new perspective with interdisciplinary characteristics for the study of ecological sustainability, and can be a reference for the ecological protection and restoration of Yanhe watershed and other similar watersheds in the Loess Plateau.