This study investigated the flux-variance relationships of temperature, water vapor, and examined the performance of this method for calculating sensible heat fluxes (Hs) and latent heat fluxes (LE) with eddy-covariance measured flux data at two different ecosystems: the oasis and the Gobi. The data are taken from “The Oasis System Energy and Water Cycles Field Experiment”, which was held in Jinta County from June 18 to July 8, 2005. Under unstable conditions, the observed standard deviation of temperature as a function of the stability parameter for the Gobi is better than the oasis. Moreover, the oasis site was found to be special, where water vapor follows flux-variance relation better than temperature. For one site, the temperature flux-variance relationship is not always better than the water vapor one, it depends on the sources/sinks distribution at the site; the Hs and LE estimations are found to be in good agreement with the measurements at the two sites, but the accuracy of Hs calculated by the flux-variance method for the Gobi is better than that for the oasis site. The calculation accuracy of LE can be improved if LE is obtained by the flux-variance method in conjunction with measured Hs.