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The Badain Jaran Desert is the second-largest area of shifting sands in China. Our first measurements of the energy components and water vapor fluxes on a megadune using eddy covariance technology were taken from April 2012 to April 2013. The results indicate that the longwave and shortwave radiative fluxes exhibited large fluctuations and seasonal dynamics. The total radiative energy loss by longwave and shortwave radiation was greater on the megadune than from other underlying surfaces. The radiation partitioning was different in different seasons. The land-atmosphere interaction was primarily represented by the sensible heat flux. The average sensible heat flux (40.1 W/m(2)) was much larger than the average latent heat flux (14.5 W/m(2)). Soil heat flux played an important role in the energy balance. The mean actual evaporation was 0.41 mm/d, and the cumulative actual evaporation was approximately 150 mm/a. The water vapor would transport downwardly and appear as dew condensation water. The amount of precipitation determined the actual evaporation. The actual evaporation was supposed to be equal to the precipitation on the megadune and the precipitation was difficult to recharge the groundwater. Our study can provide a foundation for further research on land-atmosphere interactions in this area.