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This paper aims to estimate the soil organic carbon (SOC) storage in Northeast of China, identify its balance situation and changing trends under current cropping systems, and finally put forward some strategies to keep the SOC in balance. A biogeochemical model (DNDC) for agro-ecosystem was employed to predict SOC dynamics in agricultural ecosystems at regional scale. Data on climate, soil properties, cropping systems, acreage, and management practices at county scale were collected from various sources and integrated into a GIS database to support the model runs at the regional scale.The model predicted results revealed that (1) Total SOC storage in agricultural lands in Heilongjiang, Jilin and Liaoning provinces in Northeast of China is about 1243.48 × 106 t (0-30cm soil layer), respectively occupying 58.4, 25.5 and 16.1%;(2) Under the current cultivation systems, SOC is in a situation of net loss with carbon losing at a high rate of 31.22 ×106 t a-1 (respectively 59.3, 25.9 and 14.8% in Heilongjiang, Jilin and Liaoning provinces) and 2.05 t ha-1 a-1, the situation is more serious in Heilongjiang and Jilin provinces; and (3) Protective cultivations, such as manuring, reting more residue of crop to the field, adopting no-till, are very useful for the accumulation of SOC in these regions.