Based on the eddy covariance technique, the characteristics of water and heat fluxes of two alpine wet meadow wetland ecosystems in Qinghai Lake were studied in 2015. Results showed as follows: (1) The average daily water vapor fluxes of alpine Kobresia tibetica and Kobresia humilis wet meadow wetland ecosystems were 1.74 mm and 0.99 mm, respectively, and the annual water vapor fluxes were 633.3 mm and 362.1 mm, respectively, in Qinghai lake 2015. (2) The diurnal variation of sensible heat, latent heat and net radiation all showed a single peak curve in two kinds of alpine Kobresia wet meadow wetland ecosystems, the diurnal variation maximum value of the sensible heat and latent heat occurred later than the net radiation. The maximum value of the diurnal variation of the sensible heat was 179.06 W/m2 and the minimum was 46.02 W/m2; the maximum value of latent heat was 312.55 W/m2 and the minimum was 30.58 W/m2, in K. tibetica wet meadow wetland ecosystem. The maximum value of diurnal variation of the sensible heat was 161.86 W/m2 and the minimum was 31.60 W/m2; the maximum value of latent heat was 215.44 W/m2 and the minimum was 14.08 W/m2, in K. humilis wet meadow wetland ecosystem. (3) Through the analyse of bowen ratio: the energy distribution of two alpine Kobresia wet meadow was mainly latent heat in growing season; in the non-growing season the energy distribution of K. humilis wet meadow wetland ecosystem was dominated by sensible heat, K. tibetica wet meadow wetland ecosystem was more complex. The annual energy balance rate of K. tibetica wet meadow wetland ecosystem was 0.82, and the K. humilis wet meadow wetland ecosystem was 0.89, and the increase of soil heat flux item can improve the energy balance.