ABSTRACT To investigate how the long-term application of inorganic fertilizer and organic amendments affects the accumulation of organic matter in physico-chemically fractionated components in paddy soils and how the accumulation is determined by soil properties and anthropogenic carbon input, we studied the effect of variable management of inorganic fertilizer and organic amendments for > 50 years on the amounts of accumulated soil organic carbon (SOC) in fractionated components in three paddy fields. SOC was fractionated into four components based on their physical and chemical properties: (1) light fraction (LF) derived from plant residues, (2) heavy fraction (HF) containing stable aggregates, (3) oxidizable fraction (OxF) and (4) non-oxidizable fraction (NOxF) forming organo-mineral complexes with fine-textured minerals. On average, the amount and percentage of accumulated C in the four fractions were as follows: OxF (6.63 gC kg−1 soil, 46%) > NOxF (5.32, 35) > LF (1.68, 12) > HF (1.12, 7.2), suggesting about 80% of SOC was in fine, stable fractions. The amount of accumulated C in all fractions increased slightly with the application of inorganic fertilizer, while it increased considerably with the use of organic amendments. In addition, the application of fertilizers and amendments raised the proportion of C content in LF and HF, which are labile and related to soil fertility. Stepwise multiple regression analysis using two principal component analysis scores of soil properties and anthropogenic C input further revealed that the labile fractions (LF and HF) were more strongly determined by the management of fertilizers and amendments, while the stable fractions (OxF and NOxF) were more strongly determined by soil-specific properties, mainly the amorphous nature of the soil. These results indicate that the use of certain amounts of organic amendments would be recommended to carry out rational management to improve soil fertility and C sequestration in paddy fields, with the application of amorphous minerals as an additional option.