Water use efficiency (WUE) links carbon and water exchanges between farmlands and the atmosphere. Understanding the variation and attribution of WUE is essential to reveal the physiological and ecological adaptation mechanisms of crops to the changing environment, and to better allocate, regulate and conserve water resources. However, few studies on the variation and attribution of WUE have been conducted in irrigated arid or semi-arid farmlands. Therefore, in this study, water and carbon fluxes were measured using eddy covariance systems in two farmlands (one sunflower field and one maize field) in a semi-arid irrigation district in China. It was found that the average WUE of sunflower during its full growth period was 1.72 g C kg −1 H 2 O, much lower than that of maize (4.07 g C kg −1 H 2 O). At each growth stage, the WUE of both crops were negatively correlated with vapour pressure deficit (VPD), net radiation (R n) and soil water content (SWC). The negative correlations could be attributed to the arid meteorological condition and the relatively abundant soil moisture due to irrigation and shallow groundwater levels. VPD was the main factor affecting WUE, followed by R n and SWC. It was also found that the response of WUE to crop leaf area index (LAI) and to canopy conductance (g c) depended on the VPD ranges: when VPD increased, the response of WUE to LAI and to g c decreased. Our findings could improve the understanding of the coupling effect of water and carbon fluxes over farmland ecosystems in arid and semi-arid irrigation areas and help improve agricultural production and save water resources in such areas.