Labile soil organic carbon fractions are important indicators of soil C dynamics, which is affected by different management practices. However, few studies have reported the short-term effect of a wide range of organic materials mulching on the distribution of soil total organic C (TOC) and its labile C pools in a low-productivity paddy soil. Our objective was quantify TOC and labile organic C fractions down a 0–30 cm soil profile in a 4-year field experiment receiving four organic amendments (spent mushroom compost, green manure, cattle manure and rice straw residues). Soil samples were taken from the 0–5 cm, 5–10 cm, 10–20 cm and 20–30 cm soil depths. Soil total organic carbon (TOC), total nitrogen (TN), microbial biomass C (MBC), particulate organic C (POC), potassium permanganate-oxidizable C (KMnO4-C) and dissolved organic C (DOC) were measured. Carbon management index (CMI) was also calculated. Among the four organic amendments, cattle manure showed the most profound effect on TOC, TN and labile organic C fractions and produced the highest 4-year average rice grain yield (9.67 t ha−1). The cattle manure combined with NPK resulted in the highest level of TOC (19.2 g kg−1) and TN (1.86 g kg−1) in the surface soil (0–5 cm). Additionally, KMnO4-C and MBC concentrations in the cattle manure plus NPK treatment were 1.3 and 1.5 times higher at the 0–5 cm depth, 1.4 and 1.6 times higher at the 5–10 cm depth, 1.2 and 1.4 times higher at the 10–20 cm depth compared to NPK fertilizer alone, respectively. However, POC was not sensitive to different management practices in the deeper soil layer (10–20 cm). DOC was not significantly affected by fertilization in the 0–20 cm soil layer, suggesting it was unsuitable as an early indicator of soil quality. Overall, the integrated use of cattle manure and NPK fertilizers is the most efficient management practice in improving carbon sequestering under current soil conditions. A long-term assessment is needed to confirm the most effective and sustainable management practice for improving rice grain yield and soil quality.