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Ecosystem water use efficiency (WUE) acts as an integrated functional indicator for understanding land-atmosphere interactions. The temporal patterns in the daily variations of WUE and their underlying drivers during different seasons in alpine meadow ecosystems, which are particularly vulnerable to changing climate, still remain poorly understood in spite of increasing efforts. In this study, we investigated the potential divergence in the response of WUE to climatic and biological drivers during different seasons at two alpine meadow ecosystems in the northeastern Tibetan Plateau using continuous eddy-covariance measurements of carbon and water fluxes between 2013 and 2015. We found that variations in CO2 concentration exert significantly positive effects on variations in WUE in spring, but not in summer and autumn. Notably, vapor pressure deficit (VPD) overrode other factors playing a dominant role in regulating daily variations in WUE during all seasons in these alpine meadow ecosystems. Variations in VPD explained 29.5 to 52.3% of the variance in WUE between different seasons. We further showed that carbon gain and water loss processes responded divergently to different drivers; higher VPD significantly increased ecosystem evapotranspiration; whereas, variations in soil moisture and leaf area index significantly and positively affected gross primary productivity. Our findings highlighted the increasing importance of atmospheric drought in shaping land-atmosphere interactions in alpine meadow ecosystems, particularly in a warming climate.