Based on multi-source data and using water use efficiency (WUE) as a key indicator of carbon absorption efficiency in vegetation ecosystems, a quantitative identification framework for WUE response and recovery under flash drought stress was constructed using methods such as coincidence analysis and machine learning. The spatial distribution pattern of WUE decline time and recovery time under flash drought stress during the growing season (April to September) in the Yangtze River Basin from 1982 to 2019 was evaluated, and the meteorological driving mechanism of WUE changes during the development of flash drought was quantitatively analyzed. The results indicate that the lag time of WUE response to flash drought in most areas of the Yangtze River Basin is within 1 pentad, and the sensitive areas of response are mainly distributed in the central and southeastern parts of the Yangtze River Basin. The recovery time of WUE in most areas of the Yangtze River Basin under flash drought stress is 1.5~3.5 pentads, with longer decline time and recovery time of WUE in the upper reaches of the Yangtze River. The evapotranspiration has the greatest impact on WUE during the flash drought outbreak stage, and there are significant differences in the response of WUE to meteorological factors among different types of vegetation during the flash drought recovery stage. Among them, shortwave radiation, precipitation, and evapotranspiration are the main controlling factors for WUE changes in forests, cultivated land, and grasslands, respectively.