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 CO2 fluxes in the rain-fed winter wheat field of the Chinese Loess Plateau. The results showed that the annual net ecosystem CO2 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 m(3) 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 m(3) 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.