This study investigated the flux-variance relationships of temperature, humidity, and CO2, and examined the performance of using this method for predicting sensible heat (H), water vapor (LE), and CO2 fluxes (FCO2) with eddy-covariance measured flux data at three different ecosystems: grassland, paddy rice field, and forest. The H and LE estimations were found to be in good agreement with the measurements over the three fields. The prediction accuracy of LE could be improved by around 15% if the predictions were obtained by the flux-variance method in conjunction with measured sensible heat fluxes. Moreover, the paddy rice field was found to be a special case where water vapor follows flux-variance relation better than heat does. However, the CO2 flux predictions were found to vary from poor to fair among the three sites. This is attributed to the complicated CO2 sources and sinks distribution. Our results also showed that heat and water vapor were transported with the same efficiency above the grassland and rice paddy. For the forest, heat was transported 20% more efficiently than evapotranspiration.