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The irrigated areas in the northern region of China are important food production areas. Therefore, studies on the variability of the carbon balance in these agro-ecosystems are fundamental for the management of carbon sequestration. This paper simulated the long-term variability of the carbon balance in a typical irrigated area along the lower Yellow River from 1984 to 2006, using a process-based ecosystem model called the Simple Biosphere Model, version 2. The mean annual gross primary production (GPP), mean annual net assimilation rate (NAR), mean annual soil respiration ( R), and mean annual net ecosystem exchange (NEE) were 1733, 1642, 1304, and −338 g C m a, respectively. A significant increasing trend in the seasonal total NAR during the wheat growing season, and a significant decreasing trend in the seasonal total NAR during the maize growing season were detected. However, no significant trend was found in the annual NAR, R, and NEE. The average carbon sequestration was 1.93 Tg C a when the grain harvest was not taken into account, and the carbon sequestration amount during the maize season was higher than that during the wheat season. However, the agro-ecosystem was a weak carbon source with a value of 0.23 Tg C a, when the carbon in the grain was assumed emitted into the atmosphere. [ABSTRACT FROM AUTHOR]