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• A thorough analysis on variations of CO 2 fluxes and carbon budget was conducted. • Nitrogen and water conditions were primary factors controlling maize seasonal NEE. • NBP for the winter wheat-maize rotation system ranged from -239.1 to 237.0 gCm−2. • Net ecosystem GHG emissions ranged from -39.23 to 325.23 gCm−2 for the wheat system. • Nitrogen and water application should be optimized for climate smart agriculture. Investigating CO 2 fluxes and carbon budget in agro-ecosystems is essential to develop climate smart agriculture. Here, we conducted a thorough analysis on the daily, seasonal and inter-annual variations in CO 2 fluxes and carbon budget in a winter-wheat and summer-maize rotation system in the North China Plain (NCP) to better understand the CO 2 flux exchange and the underlying mechanisms of carbon budget dynamics. During 2003-2010, the inter-annual variability of monthly gross primary productivity was significantly correlated with leaf area index (LAI), temperature and net radiation. The inter-annual variability of monthly ecosystem respiration was significantly correlated with LAI, soil temperature and moisture. Daily and monthly variability in net ecosystem exchange (NEE) was significantly correlated with LAI. At a seasonal scale, soil moisture was one of the primary factors controlling carbon sequestration of wheat system. Nitrogen application rate and water conditions were the primary factors controlling carbon sequestration of maize system. The NEE for winter wheat system, maize system, and winter wheat-maize rotation system in the NCP ranged from -418 to -29, -448 to -119, and -857 to -274 gCm−2, respectively. The net biome productivity (NBP) for winter wheat system, maize system, and winter wheat-maize rotation system in the NCP ranged from -223 to 151, -236 to 94, and -239 to 237 gCm−2, respectively. Taking greenhouse gas (GHG) emissions from irrigation, fertilization, herbicides, fungicide, insecticide, and field operations, the associated net GHG emissions ranged from -39 to 325 gCm−2 for wheat system and -22 to 287 gCm−2 for maize system. Wheat and maize systems in the region were a medium source of GHG emissions in most of years, mainly due to the large application rates of fertilization and irrigation. Our findings gain new insights into the mechanisms underlying the inter-annual variations in CO 2 fluxes and carbon budget, highlighting the optimization of genotype, environment and management interactions to realize climate smart agriculture. [ABSTRACT FROM AUTHOR]

• A thorough analysis on variations of CO 2 fluxes and carbon budget was conducted. • Nitrogen and water conditions were primary factors controlling maize seasonal NEE. • NBP for the winter wheat-maize rotation system ranged from -239.1 to 237.0 gCm−2. • Net ecosystem GHG emissions ranged from -39.23 to 325.23 gCm−2 for the wheat system. • Nitrogen and water application should be optimized for climate smart agriculture. Investigating CO 2 fluxes and carbon budget in agro-ecosystems is essential to develop climate smart agriculture. Here, we conducted a thorough analysis on the daily, seasonal and inter-annual variations in CO 2 fluxes and carbon budget in a winter-wheat and summer-maize rotation system in the North China Plain (NCP) to better understand the CO 2 flux exchange and the underlying mechanisms of carbon budget dynamics. During 2003-2010, the inter-annual variability of monthly gross primary productivity was significantly correlated with leaf area index (LAI), temperature and net radiation. The inter-annual variability of monthly ecosystem respiration was significantly correlated with LAI, soil temperature and moisture. Daily and monthly variability in net ecosystem exchange (NEE) was significantly correlated with LAI. At a seasonal scale, soil moisture was one of the primary factors controlling carbon sequestration of wheat system. Nitrogen application rate and water conditions were the primary factors controlling carbon sequestration of maize system. The NEE for winter wheat system, maize system, and winter wheat-maize rotation system in the NCP ranged from -418 to -29, -448 to -119, and -857 to -274 gCm−2, respectively. The net biome productivity (NBP) for winter wheat system, maize system, and winter wheat-maize rotation system in the NCP ranged from -223 to 151, -236 to 94, and -239 to 237 gCm−2, respectively. Taking greenhouse gas (GHG) emissions from irrigation, fertilization, herbicides, fungicide, insecticide, and field operations, the associated net GHG emissions ranged from -39 to 325 gCm−2 for wheat system and -22 to 287 gCm−2 for maize system. Wheat and maize systems in the region were a medium source of GHG emissions in most of years, mainly due to the large application rates of fertilization and irrigation. Our findings gain new insights into the mechanisms underlying the inter-annual variations in CO 2 fluxes and carbon budget, highlighting the optimization of genotype, environment and management interactions to realize climate smart agriculture. [ABSTRACT FROM AUTHOR]