Partitioning of evapotranspiration (ET) into evaporation (E) and transpiration (T) is challenging but important to better understand the mechanisms of water loss from the ground surface to the atmosphere, especially in semiarid and arid regions. In this study, the underlying water use efficiency (uWUE) method is compared with hydrometric and remote sensing-based ET partitioning methods. The uWUE method is considered to be a promising method for partitioning ET, and can also be used to obtain temporal continuous data with fine spatial representation. Thus, the uWUE method was used to partition ET in six typical ecosystems in the Heihe River basin (HRB), which is the second largest endorheic river basin in western China. During 2008–2016, the daily average contributions of T to ET (T/ET) were 0.53, 0.52, 0.59, 0.37, 0.56, and 0.59 in the alpine meadow, Qinghai spruce, maize, desert, Tamarix, and Populus euphratica–Tamarix ecosystems, respectively. The T/ET ratio exhibited obvious seasonal variations in alpine meadow, maize, Tamarix, and Populus euphratica–Tamarix ecosystems. The ET partitioning results were related to air temperature in all ecosystems, especially in areas with sufficient precipitation or irrigation water supply. The vapor pressure deficit was also a main controlling factor in the upper- and middle-reach ecosystems, especially in the Qinghai spruce ecosystem. Groundwater and/or soil moisture made high relative contributions (RCs, %) to the T/ET ratio of the riparian forest in the lower reaches. Additionally, the leaf area index also made a high RC to the T/ET ratio of deciduous vegetation. Determining the quantitative contribution of T to ET in the HRB is beneficial for water resource management to guide the rational allocation and efficient use of water resources.