As the largest lake in China, the Qinghai Lake is located in the northeast Qinghai-Tibetan Plateau and a critical transitional zone where the Asian Summer Monsoon and the Westerlies meet. The lake basin belongs to a sensitive area to global climate change and is a typically fragile ecosystem. In recent years, the wetland environment around the lake is being degenerated under the influence of natural factors and unreasonable human activities. The research on water use efficiency of alpine wetlands is helpful to clarify the degree of carbon-water coupling in alpine regions and to optimize water resources management. In this study, the changes of water use efficiency and the influence of the main environmental factors on the alpine wetlands in the two growing seasons in 2015 and 2016 were analyzed based on the eddy covariance system. The results showed that the daily variation of water use efficiency decreased at first and then increased,and the water use efficiency at the mid-stage of growing season was higher than that in the early and later stages. The seasonal variation of water use efficiency at the mid-stage of growing season was higher than that at the beginning and end of growing season, the cumulative GPPs in growth season in 2015 and 2016 were 2.69 kg·m ~(- 2) and 2.17 kg·m ~(- 2), the ETs were 496.60 kg·m ~(- 2) and 466.80 kg·m ~(- 2),and the overall water use efficiency were 5.42 g·kg ~(- 1) and 4.65 g·kg ~(- 1), respectively. The analyzed results of water use efficiency and environmental factors showed that the water use efficiency of ecosystem was significantly correlated with temperature, leaf area index,monthly precipitation and soil volume moisture content,but was poorly correlated with photosynthetically active radiation and vapor pressure deficit.