Although previous studies have illustrated the variation of CO2 fluxes in different terrestrial ecosystems, more needs to be reported on desert ecosystems. This study, based on the eddy covariance (EC) measurements data over the Gurbantunggut Desert, analyzed the controlling factors and variations of net ecosystem exchange (NEE), gross primary production (GPP), and ecosystem respiration (Reco) during the growing season (April-September2021) in Gurbantunggut Desert. The results were as follows: 1) Carbon fluxes in the Gurbantunggut Desert had prominent daily and seasonal variations during the growing season. On the daily scale, it showed a net uptake during the day and a net release at night, and the monthly average daily change curve of NEE was “U” shaped; on the seasonal scale, carbon uptake was observed in all months, with a peak of −37.76 gC m−2 month−1 in May. 2)The cumulative amounts of NEE, GPP, and Reco in the Gurbantunggut Desert were −193.74, 235.43, and 41.69 g C m−2, respectively, throughout the growing season, showing carbon sinks. 3) Correlation analysis with environmental factors revealed that NEE, GPP, and Reco of desert ecosystems were highly significantly correlated with photosynthetically active radiation (PAR) at different time scales (p