Ecosystem water use efficiency (WUE describes carbon-water flux coupling in terrestrial ecosystems. Understanding response and resilience of WUE to drought are essential for sustainable water resource and ecosystem management under increasing drought risks over China due to climate warming. Here we analyzed the response of ecosystem WUE to drought (spatiotemporal variability and resilience) over China during 1982–2015 based on an evapotranspiration (ET) dataset based on the model tree ensemble (MTE) algorithm using flux-tower ET measurements and satellite-retrieved GPP data. The results showed that the multiyear average WUE was 1.55 g C kg−1 H2O over China. WUE increased in 77.1% of Chinese territory during the past 34 years. During drought periods, the ecosystem WUE increased mainly in the northeast of Inner Mongolia, Northeast China and some regions in southern China with abundant forests but decreased in northwestern and central China. An apparent lagging effect of drought on ecosystem WUE was observed in the east of Inner Mongolia and Northeast China, the west and east regions of North China and the central part of Tibetan Plateau. Some ecosystems (e.g., deciduous needle-leaf forests, deciduous broadleaf forests, evergreen broadleaf forests and evergreen needle-leaf forests) in Central China, Northeast and Southwest China exhibited relatively greater resilience to drought than others by improving their WUE. Our findings would provide useful information for Chinese government to adopt a reasonable approach for maintaining the structure and functions of ecosystems under drought disturbance in future.