To accurately evaluate the carbon sequestration potential and better elucidate the relationship between the carbon cycle and regional climate change, using eddy covariance system, we conducted a long-term measurement of CO 2 fluxes in the rain-fed winter wheat field of the Chinese Loess Plateau. The results showed that the annual net ecosystem CO 2 exchange (NEE) was (-71.6±5.7) and (-65.3±5.3) g C m-2 y-1 for 2008-2009 and 2009-2010 crop years, respectively, suggesting that the agro-ecosystem was a carbon sink (117.4-126.2 g C m-2 yr-1). However, after considering the harvested grain, the agro- ecosystem turned into a moderate carbon source. The variations in NEE and ecosystem respiration (R eco ) were sensitive to changes in soil water content (SWC). When SWC ranged form 0.15 to 0.21 m3 m-3, we found a highly significant relationship between NEE and photosynthetically active radiation (PAR), and a highly significant relationship between R eco and soil temperature (T s ). However, the highly significant relationships were not observed when SWC was outside the range of 0.15-0.21 m3 m-3. Further, in spring, the R eco instantly responded to a rapid increase in SWC after effective rainfall events, which could induce 2 to 4-fold increase in daily R eco , whereas the R eco was also inhibited by heavy summer rainfall when soils were saturated. Accumulated R eco in summer fallow period decreased carbon fixed in growing season by 16- 25%, indicating that the period imposed negative impacts on annual carbon sequestration.