Abstract: Farmland ecosystems exhibit dual attributes of carbon sources and carbon sinks. Reducing carbon emissions while enhancing carbon uptake is essential for sustainable agricultural development. This study selected the black soil region of Northeast China as the research area. We investigated the spatio-temporal changes of carbon emissions and uptake, as well as carbon surplus from 2000 to 2020. On this basis, we calculated the carbon footprint and analyzed the contributions of influencing factors to carbon emissions and uptake to characterize the spatio-temporal dynamics and drivers of the carbon budget in the Northeast Black Soil Region and provide a scientific basis for targeted carbon management strategies. The results showed that carbon emissions and uptake increased by 108.18% and 136.89%, respectively, while the farmland ecosystem showed a net carbon sink status from 2000 to 2020. Rice (Oryza sativa) cultivation was the largest contributor to total carbon emissions, whereas chemical fertilizers were the dominant source of carbon emissions from agricultural inputs. Carbon uptake mainly came from corn (Zea mays) and rice. The spatial patterns of carbon emissions, carbon uptake, and carbon footprint were relatively consistent, showing a mid-high, peripheral-low pattern. The carbon footprint per unit area decreased by 3%, indicating that grain production became less dependent on external inputs and moved toward greater sustainability. Agricultural industrial structure, urbanization level, and agricultural production efficiency suppressed carbon emissions, while regional economic development level, regional industrial structure, and rural population had the opposite effects. Among the influencing factors of carbon uptake, carbon uptake structure had a negative effect, while carbon uptake coefficient, carbon uptake technology level and labor force size promoted carbon uptake. Overall, this study reveals the spatio-temporal evolution of carbon emissions and uptake and highlights the need to consider policy continuity and spatial differences in driving factors. We recommend adopting efficient fertilization as a key strategy for reducing emissions, shifting away from the traditional production methods that heavily rely on extensive inputs. By optimizing industrial structure and improving agricultural production efficiency, along with scaled management, we can achieve a win-win outcome for food production and environmental protection. This study provides an important basis for formulating sustainable agricultural development policies and low-carbon plans in grain-producing areas.