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Soil organic carbon (SOC) sequestration in response to long-term fertilizer management practices under jute-rice-wheat agro-ecosystem in alluvial soils was studied using a modeling approach. Fertilizer management practices included nitrogen (N), phosphorus (P) and potassium (K) fertilization, manure application, and root-stubble retention of all three crops. Soil carbon (C) model RothC was used to simulate the critical C input rates needed to maintain initial soil C level in long timescale (44 years). SOC change was significantly influenced by the long-term fertilizer management practices and the edaphic variable of initial SOC content. The effects of fertilizer combination 100%NPK+FYM on SOC changes were most significant over 100%NPK fertilization. If the 100% NPK fertilizer along with manure applied with stubble and roots retention of all crops, alluvial soils of such agro-ecosystem would act as a net C sink, and the average SOC density kept increasing from 18.18 Mg ha(-1) during 1972 to the current average of approximate to 22 Mg ha(-1) during 2065 s. On an average, the critical C input was estimated to be 5.30 Mg C ha(-1) yr(-1), depending on local soil and climatic conditions. The critical C input could be effectively estimated using a summary model driven by current SOC level, mean annual temperature, precipitation, and soil clay content. Such information will provide a baseline for assessing soil C dynamics under potential changes in fertilizer and crop residues management practices, and thus enable development of management strategies for effectively mitigating climate change through soil C sequestration.