Several flux stations at difference sufaces have been established for the project “Simultaneous remote sensing and ground based experiment in the Heihe River basin”. In this paper, we selected the observation data on grasslands, forests and farmland and analyzed the characteristics of water vapor, heat and carbon dioxide (CO2) fluxes. The results showed that there are obvious diurnal and seasonal variations of energy balance components (net radiation, sensible heat, latent heat and soil heat flux, etc.) and different surface in the Heihe River basin has distinct characteristics. The Eddy-Covariance (EC) flux data have been compared with Large Aperture Scintillometer (LAS) observations at Arou Station (in the upper Heihe Basin) and Linze Station (in the middle basin). Both have good correlations, however, the sensible heat fluxes observed by LAS are generally larger than that of EC. The differences are mainly from the different footprints′ or source areas of LAS and EC in the non-uniform surfaces of the specific station. Besides, LAS observation of heat flux may comprise contributions from larger scale atmospheric turbulence. By considering soil heat storage in the upper soil layers, the surface energy balance closure has also been analyzed in each station.