The carbon and water cycle, an important biophysical process of terrestrial ecosystems, is changed by anthropogenic revegetation in arid and semiarid areas. However, there is still a lack of understanding of the mechanisms of carbon and water coupling in intrinsic ecosystems in the context of human activities. Based on the CO₂ and H₂O flux measurements of the desert steppe with the planted shrub Caragana liouana, this study explored the carbon and water flux coupling of the ecosystem by analyzing the variations in gross primary productivity (GPP), evapotranspiration (ET) and water use efficiency (WUE) and discussing the driving mechanisms of biological factors. The seasonal variation in climate factors induced a periodic variation pattern of biophysical traits and carbon and water fluxes. The GPP and ET fluctuated in seasons, but the WUE was relatively stable in the growing season. The GPP, ET and WUE were significantly driven by global radiation (R_g), temperature (T_a and T_s), water vapor pressure deficit, leaf area index and plant water stress index (PWSI). However, R_g, temperature and PWSI were the most important factors regulating WUE. R_g and temperature directly affected WUE with a positive effect but indirectly inhibited WUE by rising PWSI. Plant water stress inhibited photosynthesis and transpiration of the planted shrub community in the desert steppe. When the plant water stress exceeded a threshold (PWSI >0.54), the WUE would decrease since the GPP responded more quickly to the plant water stress than ET. Our findings suggest that policies related to large-scale carbon sequestration initiatives under afforestation must first fully consider the status of water consumption and WUE.