As a new flux measuring instrument, Large Aperture Scintillometer (LAS), which can measure sensible heat flux in large scales, has developed rapidly in recent years. A great number of ground stations were established over different surfaces in the upper and middle reaches of Heihe river basin, supported by the project “Watershed Airborne Telemetry Experimental Research (WATER)”. In addition to conventional meteorological parameters, radiation components, soil temperature/soil moisture, soil heat flux and Eddy Covariance system (EC), large aperture scintillometers were erected in the Arou freeze/thawing observation station (upper reaches) and Linze grassland station (middle reaches). This paper focused on the analysis of the diurnal and seasonal variations of sensible heat flux measured by LAS, and used the observation data from March, 2008 to December, 2009 at Arou station and from May to August, 2008 at Linze grassland station. In order to improve the overall quality of LAS measurements, analyzing carefully not only the difference of EC and LAS source area (based on analytical models) and the relevant influences, but also the quality control of LAS measurement data under different atmosphere stabilities and the calculation methods of sensible heat flux by the relative analysis with EC data were analyzed carefully. Long-term data analysis showed that: There were good correlations in sensible heat flux and its time variation between LAS and EC measurements. There were also significant differences in part time, which was caused mainly by the different underlying surfaces in their source areas. In most cases, the LAS measurements were on average larger than the EC′s. The reason seems that EC has a smaller source area than LAS, whose measurement has the effect of a natural area averaged fluxes.