Abstract Partitioning evapotranspiration (ET) into evaporation ( E ) and transpiration ( T ) is essential for understanding the global hydrological cycle and improving water resource management. However, ecosystem‐level ET partitioning remains challenging. Here we proposed a novel ET partitioning method that uses the unified stomatal conductance model to estimate T :ET by calculating the ratio of the ecosystem water use efficiency (WUE eco ) to leaf WUE (WUE leaf ) using half‐hourly flux data. The WUE leaf values estimated by the unified stomatal conductance model agree with an independently measured ratio of hourly photosynthetic rate to T rate ( R 2 = 0.69). The sensitivity of T :ET to the key parameter g 1 varied among different plant functional types (PFTs), but the T :ET variations for each PFT were all controlled within 20% when g 1 altered within its 95% confidence interval. The mean annual T :ET was highest for evergreen broadleaf forests (0.63), followed by deciduous broad forests (0.62), grasslands (0.52), evergreen needleleaf forests (0.43) and woody savannas (0.40). C 3 croplands had higher T :ET (0.65) than C 4 croplands (0.48). Seasonal variations in T :ET varied across PFTs and the leaf area index explained about 50% of the variation in seasonal T :ET. Our method is not only consistent with other three EC‐based methods: Z16, N18, and L19 ( R = 0.92, 0.94, and 0.68), but also shows high correlations to sap flow‐based T ( R = 0.70) at three different forest sites. The method developed in this study provides a feasible and universal approach for ET partitioning of global EC sites, improving the understanding of ecosystem T characteristics across climates and PFTs.