Based on the data of the flux observation system of the Shouxian National Climate Observatory from July 2007 to June 2008, an analysis is made of the interaction processes between atmosphere and land in the cropland ecosystem over the Huaihe River basin. The absent ratios of the gradient and eddy data are calculated, and the flux gradient and eddy covariance methods are adopted to validate the credibility of the data, and then the seasonal and daily variation of the CO2 flux, latent heat flux and sensible heat flux, as well as the relationship between the surface and those fluxes, are analyzed. Meanwhile the mean surface albedo, energy budget closure rate and drag coefficient are calculated. The results show that the observation data is credible; the original data is objective and useable; there exists seasonal variation obviously in these fluxes; these fluxes have close relationship with the condition of the underlying surface; and the daily variation of fluxes shows a single peak distribution. The mean surface albedo, mean energy budget closure rate and drag coefficient calculated by the data from the flux observation system are 0.18, 0.92, and 0.0092, respectively, in the Huaihe River basin.