In China, croplands account for a relatively large form of vegetation cover. Quantifying carbon dioxide exchange and understanding the environmental controls on carbon fluxes over croplands are critical in understanding regional carbon budgets and ecosystem behaviors. In this study, the net ecosystem exchange (NEE) at a winter wheat/summer maize rotation cropping site, representative of the main cropping system in the North China Plain, was continuously measured using the eddy covariance technique from 2005 to 2009. In order to interpret the abiotic factors regulating NEE, NEE was partitioned into gross primary production (GPP) and ecosystem respiration (Reco). Daytime Reco was extrapolated from the relationship between nighttime NEE and soil temperature under high turbulent conditions. GPP was then estimated by subtracting daytime NEE from the daytime estimates of Reco. Results show that the seasonal patterns of the temperature responses of Reco and light-response parameters are closely related to the crop phenology. Daily Reco was highly dependent on both daily GPP and air temperature. Interannual variability showed that GPP and Reco were mainly controlled by temperature. Water availability also exerted a limit on Reco. The annual NEE was −585 and −533 g C m−2 for two seasons of 2006–2007 and 2007–2008, respectively, and the wheat field absorbed more carbon than the maize field. Thus, we concluded that this cropland was a strong carbon sink. However, when the grain harvest was taken into account, the wheat field was diminished into a weak carbon sink, whereas the maize field was converted into a weak carbon source. The observations showed that severe drought occurring during winter did not reduce wheat yield (or integrated NEE) when sufficient irrigation was carried out during spring.