Under global climate change, more frequent and widespread droughts have dramatic impacts on the water and carbon cycles. Water use efficiency (WUE) is a commonly used indicator reflecting the trade‐off relationship between carbon sequestration and water consumption. Therefore, this study aims to clarify the variations in WUE and the effects of drought on WUE in sensitive alpine meadows on the Tibetan Plateau. Based on 6‐year (2013–2018) continuous carbon and water flux data observed by the eddy covariance system, WUE was calculated by gross ecosystem productivity (GEP)/evapotranspiration (ET). WUE followed a unimodal variation with time during growing seasons in the years without droughts. However, drought disrupted this pattern by its effects on the coupled relationship between carbon and water fluxes. Specifically, droughts showed divergent effects on WUE variations in different periods of the growing seasons. In the early‐growing seasons, droughts induced an increase in WUE. During this period, WUE was mainly regulated by temperature and leaf area index (LAI), and the GEP was low due to the smaller LAI. Therefore, the drought‐induced reduction in GEP was less than that in ET; thus, WUE increased. In the mid‐growing seasons, droughts depressed WUE. WUE was dominated by water conditions and the LAI during this period. When drought occurred, GEP decreased faster than ET, and hence, WUE decreased. In the late‐growing season, WUE was mainly driven by temperature and the LAI, but short‐term drought slightly enhanced WUE. These results are helpful in understanding the responses of fragile alpine ecosystems to future climate change.