Alpine meadow is one of the most widely distributed vegetation types on the Tibetan Plateau—the Earth’s Third Pole. Characterizing the carbon and water vapor fluxes in alpine meadow ecosystems is of particular importance for elucidating the mechanisms underlying the carbon budget and water cycle in high-altitude areas, especially under changing climatic conditions. Thus, the quantitative relationships between carbon and water fluxes and environmental drivers were examined based on a continuous eddy covariance (EC) dataset from 2013 to 2015 over the alpine Kobresia meadow on the northeastern Tibetan Plateau. The results show that (1) the net ecosystem CO2 exchange (NEE) was − 152.89 g C m−2 year−1, − 197.69 g C m−2 year−1, and − 160.09 g C m−2 year−1 from 2013 to 2015, respectively, suggesting that this alpine meadow ecosystem is a strong and consistent carbon sink. (2) Both the multiple stepwise regression analysis (MSRA) and the structural equation model (SEM) analysis confirmed the dominant role of Ts in controlling the carbon flux and that of Rn in controlling the water vapor flux. (3) The inherent water use efficiency (IWUE = GPP×VPD/ET) and underlying water use efficiency (uWUE = GPP×VPD0.5/ET), which incorporates the vapor pressure deficit (VPD) effect, better described the carbon-water coupling characteristics at daily and hourly scales than did the traditional water use efficiency (WUE = GPP/ET). These findings highlight the dominant climatic factors controlling CO2 and water vapor exchanges and contribute to our knowledge of the land surface-atmosphere exchange in alpine meadows on the Tibetan Plateau.