We studied the seasonal variation in carbon dioxide, energy and water vapor fluxes over a saline desert in western China using the eddy covariance technique. The plant community over the desert consisted of an over-storey dominated by T. ramosissima with sparse under-storey herb plants. Measurements presented here cover 6 month period from May to October. The following questions were addressed: (1) How did Rn, Fc, LE and H varied seasonally? (2) How did Fc and LE responded to environmental factors after raining events? (3) How did WUE varied after raining events? LE, Rn, and Fc exhibited a clear seasonal pattern. But H did not. Rn was highest (120-160W/m2) in mid-summer (June-August); the daily average of Rn was 72.87 28.3 W/m2. The daily average of H was 40.8 23 W/m2. In contrast, values of LE were very low (<30W/m2), and peak values appeared after rainfall, the daily average of LE was 29 13.3W/m2. Obviously all available energy was dissipated as sensible, rather than latent heat. In early May 2004, new leaf development was in progress, the respiratory processes were dominating, and the Saline Desert was a weak sink of carbon flux. By late May, plant came into the rapid growth; strong net sink activity started and lasted until the end of September. At the end of October the Saline Desert was net source of carbon. For the entire growing period, the Saline Desert was a weak sink, with a net sink estimated at only about -136mg/m2. During wet and dry periods after rain events, Fc displayed no obvious difference, the relationship between Fc and photosynthetically active radiation was described well by a hyperbolic fit, with the r2 values greater than 0.70, there appeared to be only PAR effect on Fc. However, in contrast to latent heat flux, variation in LE was rather different during the two periods. In wet period, the size of the rainfall pulse was positively related to the magnitude of the flux, the peak daytime LE was 238W/m2 whereas the maximum LE was approximately 100W/m2 in dry period, there appeared to be precipitation effect on LE. Low ecosystem WUE values measured during the wet period may be explained by soil evaporation, which resulted in the enhancement of LE.