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Rice-wheat (R-W) rotation systems are ubiquitous in South and East Asia, and play an important role in modulating the carbon cycle and climate. Long-term, continuous flux measurements help in better understanding the seasonal and interannual variation of the carbon budget over R-W rotation systems. In this study, measurements of CO fluxes and meteorological variables over an R-W rotation system on the North China Plain from 2007 to 2010 were analyzed. To analyze the abiotic factors regulating Net Ecosystem Exchange (NEE), NEE was partitioned into gross primary production (GPP) and ecosystem respiration. Nighttime NEE or ecosystem respiration was controlled primarily by soil temperature, while daytime NEE was mainly determined by photosythetically active radiation (PAR). The responses of nighttime NEE to soil temperature and daytime NEE to light were closely associated with crop development and photosynthetic activity, respectively. Moreover, the interannual variation in GPP and NEE mainly depended on precipitation and PAR. Overall, NEE was negative on the annual scale and the rotation system behaved as a carbon sink of 982 g C m per year over the three years. The winter wheat field took up more CO than the rice paddy during the longer growing season, while the daily NEE for wheat and rice were -2.35 and -3.96 g C m, respectively. After the grain harvest was subtracted from the NEE, the winter wheat field became a moderately strong carbon sink of 251-334 g C m per season, whereas the rice paddy switched to a weak carbon sink of 107-132 per season. [ABSTRACT FROM AUTHOR]