Spring wheat (Triticum aestivum Linn.) is an important crop for food security in the desert-oasis farmland in the middle reaches of the Heihe River in northwestern China. We measured fluxes using eddy covarianceand meteorological parameters to explore the energy fluxes and the relationship between CO² flux and climate change in this region during the wheat growing seasons in 2013 and 2014. The energy balance closures were 70.5% and 72.7% in the 2013 and 2014 growing season, respectively. The wheat ecosystem had distinct seasonal and diurnal dynamics of CO² fluxes with U-shaped curves. The accumulated net ecosystemic CO² exchanges (NEE) were −111.6 and −142.2 g C/m² in 2013 and 2014 growing season,respectively. The ecosystem generally acted as a CO² sink during the growing season but became aCO² source after the wheat harvest. A correlation analysis indicated that night-time CO² fluxes wereexponentially dependent on air temperature and soil temperature at a depth of 5 cm but were notcorrelated with soil-water content, water-vapour pressure, or vapour-pressure deficit. CO² flux was notcorrelated with the meteorological parameters during daytime. However, irrigation and precipitation,may complicate the response of CO² fluxes to other meteorological parameters.