Soil carbon pools play a major role in sustaining agro-ecosystems and maintaining environmental quality as they act as a major source and sink of atmospheric carbon. The long-term effect of manuring and fertilization on accessibility of carbon pools of soil in high intensity rice (Oryza sativa L.)−potato (Solanum tuberosum L.)−wheat (Triticum aestivum L.) and maize (Zea mays L.) −potato−onion (Allium cepa L.) cropping systems in Inceptisol of semi-arid sub-tropical India continuing for 10 years was studied. Soil samples were collected (0-15 and 15-30 cm soil depth) from the treatments comprising control (T1), 100% NPK-Fertilizer (T2), 100% N-Vermicompost (VC) (T3), 50% NPK-Fertilizer + 50% N-Vermicompost (VC) (T4), 100% NPK-Fertilizer + crop residue (CR) (T5), 100% N-Vermicompost + CR (T6). Assessment of carbon pools was done by estimating total soil C (TSC), total soil nitrogen (TSN), C:N ratio, carbon mineralization (Cmin), total polysaccharide (TP) and relationship between these pools. The results showed that the application of 100% N-VC (T3) and 100% N-VC + CR (T6) increased the TSC by 94% and 80%, respectively, over 100% NPK in rice-potato-wheat cropping system, while in maize-potato-onion system, 100% N-VC (T3) increased TSC by 48% over 100% NPK (T2) at 0-15 cm soil depth. The soil C:N ratios were generally wider in case of treatments receiving organic sources. In both the soil depths, the T6 treatment (100% N-VC + CR) had resulted higher C mineralization than the other treatments throughout the incubation period. The stable C was lower in maize–potato–onion system than that in the rice–potato–wheat system. The total polysaccharides was higher in organic amended treatments (T6, T3) over chemical fertilizer treatments in improving the TP content in soil which was related to greater C input.