Efforts to develop effective climate strategies necessitate a better understanding of the relationship between terrestrial water and carbon cycles. Water use efficiency (WUE) has been often used to characterize this relationship, while the role of transpiration (T) in the variation of ecosystem WUE has been less investigated. Here, we partitioned WUEET (the ratio of gross primary productivity (GPP) to evapotranspiration (ET)) into a two-component process, i.e., the ratio of gross primary productivity to plant transpiration, GPP/T, that is WUET, and the ratio of plant transpiration to evapotranspiration, T/ET. Based on two GPP datasets (i.e., GPP based on the light use efficiency model or the vegetation index- NIRv) and the GLEAM ET dataset, this study investigated the role of T in the variation of WUE in the ecosystem level and how the role is affected by drought. We found that drought can lead to the change of ET partitioning, thus affecting the variability of WUE. The variability of WUEET was dominated by WUET. In general, the proportion of T increased gradually from humid to arid areas. To adapt to drought conditions, vegetation in arid areas tend to have a high stress resistance by increasing their WUE. We further found that WUET has stronger seasonal stability than WUEET. GPP dominated WUEET variability in humid/sub humid areas, while ET and GPP jointly dominated WUEET variability in semi-arid/arid areas. GPP dataset based on light use efficiency (LUE) could better reflect the impact of drought on vegetation. This study contributes to a better understanding of the change mechanism of ecosystem WUE and emphasizes the critical role of physiological process components in water-carbon cycling.