The rice-wheat cropping system under Vertisol in sub-tropical regions of India faces significant challenges in maintaining soil health and achieving sustainable yields. This is primarily due to climatic variability and intensive agricultural practices, which accelerate the loss of soil organic carbon (SOC) and lead to soil degradation. There is a pressing need to adopt sustainable nutrient management, that not only maximize crop yields but also support climate change mitigation through carbon (C) sequestration and soil health management. In this context, a long-term fertilizer management (25 years) study was undertaken to assess crop productivity, C fractions, sequestration potential to achieve soil C 4 per mille under rice-wheat cropping system in sub-tropical Vertisol. The experiment was based on ten different fertilizer treatments either alone or in combination with organics. Grain yield, system productivity, and the sustainable yield index (SYI) were significantly higher under the 150%NPK and NPK + Farmyard manure (FYM) treatments compared to the unfertilized control. Relying on imbalanced fertilization (N) is inadequate for long-term sustainability. Long-term application of 100% NPK+FYM increased SOC content by up to 16%, whereas it decreased by 34% under absolute control relative to the initial value. Integrated nutrient management (INM) significantly enhanced the SOC pools, with higher proportion (57%) of total SOC in passive C pools. The increase in SOC stock was significantly correlated (R2 = 0.76) with system productivity, requiring a minimum C input of 2.7 Mg C ha-1 yr-1 to maintain C equilibrium. The INM treatment achieved the highest C sequestration (2.27 Mg ha-1), potential (7.04 Mg ha-1) and rate (0.10 Mg C ha-1 yr-1) compared to NPK. In the present study, the C sequestration rate under NPK+FYM and 150%NPK surpassed the annual increment requirement of 0.4% SOC to achieve the target of the “4 per mille”. Over 25 years, application of 5 Mg ha-1 FYM with NPK proved to be the most sustainable practice for SOC management. In addition to enhancing SOC stock, this practice maximizes crop productivity, thereby highlighting the potential of soil management as an effective voluntary carbon sequestration pathway for climate-change mitigation strategy in sub-tropical regions.