Soil labile (biologically active) organic carbon fractions under different crop rotation systems in Jiangsu Province, China, were investigated after 10 years of rotation. The rotation systems, including green manurerice-rice (GmRR), wheat-rice-rice (WRR), wheat-rice (WR) and wheat/corn intercrop-rice (WCR) rotations,were established on paddy soils using a randomized complete block design with three replicates. The total organic carbon (TOC), total nitrogen (TN) and water-soluble organic carbon (WSOC) in the soils under different systems were greater in the GmRR and WRR than in the WR and WCR rotation systems because the soils under triple cropping often received more crop residues than the soils under double cropping. Both the WSOC and the microbial biomass carbon (MBC) contents in the soils of the GmRR rotation system were significantly greater than those in the other crop rotation systems, which was due to the return of green manure to the fields of the GmRR rotation system. The results of a 13C nuclear magnetic resonance (13C-NMR) analysis indicated that the structural characteristics of soil WSOC were similar under the four crop rotation systems with carbohydrates and long-chain aliphatics being the major components. Correlation analysis showed that the content of the WSOC was positively correlated with that of the MBC (P ＜0.01),and all had significantly positive correlations with TOC and TN. The coefficients of variation (CVs) for WSOC and WSOC/TOC were greater than the other indices (e.g, MBC, TOC and TN), suggesting that WSOC in the soils was more sensitive to these rotation systems. The results above indicated that the soil amended with green manure could not only increase the usable C source for soil microorganisms, but could also enhance soil organic matter content; hence, rotation with green manure would be a good strategy for sustainable agriculture.