Plants in arid regions possess unique physiological mechanisms to conserve water and resist drought, which are crucial for their survival and growth. However, the trend of WUE along the drought gradient and its relationships with plant physiological and ecological factors and environmental factors in high-altitude desert areas remain unclear. In this study, we selected nine typical shrubs from Golmud, Nomuhong, Da Qaidam, Delhi, and Dulan as research subjects, measured the instantaneous and intrinsic water use efficiency of different plants using the gas exchange method, and used the δ¹³C value to represent the long-term water use efficiency of plants. We analyzed the response characteristics of water use efficiency to plant physiological and ecological factors and environmental factors using Pearson correlation analysis and redundancy analysis. The results showed that both instantaneous and intrinsic water use efficiency were significantly positively correlated with δ¹³C at both community and species scales (P < 0.05). Water use efficiency showed an overall increasing trend with the increase of drought degree. There are significant differences in water use efficiency between different species, and Calligonum korlaense, as a C₄ species, its long-term, instantaneous and intrinsic water use efficiency were higher than other C₃ species. The influence of plant physiological and ecological factors on water use efficiency is stronger than that of soil physical and chemical properties and climate factors, which explained 91.14%, 35.64%, and 39.68% of the overall variation in water use efficiency, respectively. Among them, the intercellular CO₂ concentration (Ci), leaf net photosynthetic rate (A) and soil total phosphorus (STP) have the greatest influence on water use efficiency, with explanatory power of 15%, 10.8%, and 8.3%, respectively. The results are of great significance for understanding the characteristics and physiological and ecological mechanisms of water use efficiency of typical desert plants in high altitude desert areas.