Labile soil organic carbon (SOC) pools, estimated through chemical fractionation techniques, are considered sensitive indicators of management-induced changes in quality and composition of soil organic matter. Although the impacts of organic manure and crop residue applications on C sequestration in rice-wheat system are fairly well documented, their influence on labile SOC pools is relatively less known. Impacts of organic manure, rice straw, and inorganic fertilizer nitrogen (N) applications on soil total organic carbon (TOC) and SOC pools including water-extractable organic C (WEOC), hot water-soluble organic C (HWOC), potassium permanganate-oxidizable organic C (KMnO4-C), microbial biomass C (MBC), mineralizable organic C (Cmin), and the oxidizable fractions of decreasing oxidizability (easily-oxidizable, oxidizable, and weakly-oxidizable) were investigated in an 11-year field experiment under rice-wheat system. The field experiment included treatments of different combinations of farmyard manure, rice straw, and fertilizer N application rates, with C inputs estimated to be in the range from 23 to 127 Mg ha−1. After 11 years of experiment, WEOC, HWOC, and KMnO4-C were 0.32%–0.50%, 2.2%–3.3%, and 15.0%–20.6% of TOC, respectively. The easily-oxidizable, oxidizable, and weakly-oxidizable fractions were 43%–57%, 22%–27%, and 10%–19% of TOC, respectively. The applications of farmyard manure and rice straw improved WEOC, HWOC, KMnO4-C, easily-oxidizable fraction, Cmin, and MBC, though the rates of change varied considerably from –14% to 145% and –11% to 83% of TOC, respectively. At the C input levels between 29 and 78 Mg C ha−1 during the 11-year period, the greatest increase was observed in WEOC and the minimum in KMnO4-C. Water-extractable organic C exhibited a relatively greater sensitivity to management than TOC, suggesting that it may be used as a sensitive indicator of management-induced changes in soil organic matter under rice-wheat system. All the other labile SOC pools exhibited almost the same sensitivity to management as TOC. Most of the SOC pools investigated were positively correlated to each other though their amounts differed considerably. Long-term applications of farmyard manure and rice straw resulted in build-up of not only the labile but also the recalcitrant pool of SOC, emphasizing the need for continued application of organic amendments for permanence of the accrued C under the experimental conditions.