Water Use Efficiency (WUE) is an important indicator of the carbon cycle in the hydrological and ecological system. It is of great significance to study the response of different hydrological processes to climate and to understand ecosystem carbon sink. However, little is known about the effects and mechanisms of precipitation and temperature on the WUE of different hydrological processes. Thus, three kinds of WUEs (GPP/E (eWUE), GPP/Et (tWUE), and GPP/P (pWUE)) are defined for three different hydrological indicators in semi-arid areas in this study in order to reveal the variation pattern of WUEs based on hydrological indicators and their response to climate. We found that in the past 15 years, the seasonal fluctuation of evapotranspiration in arid areas was large, and the spatial difference of WUE of different hydrological processes was obvious. In semi-arid areas, temperature had a significant effect on WUE (about 68–81%). However, precipitation had a lag effect on WUEs, and the negative impact of precipitation has a great influence (about 84–100%). Secondly, the threshold values of precipitation to WUEs (200 or 300 mm) and temperature to WUEs (2 or 7 °C) are also different from previous studies. This study advances our understanding of the influence of different hydrological processes on ecosystem carbon and climate.