Interannual variability (IAV) in net ecosystem carbon production (NEP) plays an important role in the processes of the carbon cycle, but the long-term trends in NEP and the climatic and biotic control of IAV in NEP still remain unclear in agroecosystems. We investigated interannual variability in NEP, expressed as annual values and anomalies, and its climatic and biotic controls using an eddy-covariance dataset for 2005–2018 for rain-fed spring maize in northeastern China. Average annual NEP was 270±31 g C m−2yr −1, with no significant changes over time. The effects on interannual variability in NEP of gross ecosystem productivity (GEP) that was mainly controlled by soil water content (SWC) and leaf area index (LAI), were more than those of respiration (RE) that was controlled by temperature and LAI. Further, maximum daily NEP (NEPmax) that was dominated by summer vapor pressure deficit explained the largest fraction of annual anomalies in NEP, followed by carbon dioxide uptake period (CUP) that was defined by the beginning date (BDOY) and the end date (EDOY) of CUP. The variability in BDOY was mainly determined by spring precipitation and the effective accumulated temperature, and the variability in EDOY was determined by autumn precipitation, SWC and LAI. NEP may decrease with declining precipitation in the future due to decreasing GEP, NEPmax, or CUP, and irrigation and residues cover may be useful in efforts to maintain current NEP levels. Our results indicate that interannual variability in NEP in agroecosystems may be more sensitive to changes in water conditions (such as precipitation, SWC and VPD) induced by climate changes, while temperature may be an important indirect factor when VPD is dominated.