Abstract: This study aims to investigate the distribution characteristics of organic carbon (OC) and total nitrogen (TN) in water-stable aggregates, silt and clay fractions, in order to gain a deep understanding the sequestration mechanism of soil organic carbon (SOC) under various fertilization regimes. Topsoil samples (0-20 cm) were collected from the raw soil and reclaimed soil under different fertilization regimes of six consecutive ages. A wet sieving method was used to fractionate the particle size in soil, including the large macroaggregates (> 2 mm), small macroaggregates (0.25-2 mm), microaggregates (0.053-0.25 mm), as well as the silt- and clay-sized fractions (< 0.053 mm). The contents of OC and TN were analyzed for the water-stable aggregates, the silt and clay fractions. A systematic experiment was also carried out to reveal the driving factors for the changes of SOC storage, while, the relationship between crop yields and the OC content in the water-stable aggregates, the silt and clay fractions. Four treatments were selected, including no fertilizer (control, CK), nitrogen, phosphorus, and potassium fertilizer (NPK), single application of organic manure (M), and the combined application of organic manure and synthetic fertilizers (MNPK). The results showed that the contents of OC and TN were similar in macroaggregates and microaggregates, particularly higher than that in the silt and clay fractions. Compared with the raw soil, the CK, NPK and M treatments significantly increased the OC contents in the 0.25-2 mm, 0.053-0.25 mm aggregates, and the < 0.053 mm fractions, with the increase of 97.96%, 66.19% and 97.60% (CK), 87.07%, 92.09%, 92.80% (NPK), and 95.24%, 148.20%, 112.00% (M), respectively. The MNPK treatment significantly increased the OC contents in > 2, 0.25-2, 0.053-0.35 mm aggregates, and the < 0.053 mm fractions, with the increase of 151.88%, 160.54%, 135.25%, and 92.80%, respectively. In addition, the CK, NPK, M and MNPK treatments significantly increased the TN contents in > 2 mm, 0.25-2 mm and 0.053-0.25 mm aggregates, with the increase of 43.66%, 46.78%, and 29.95% (CK), 41.83%, 52.35%, 30.43% (NPK), 52.81%, 50.43%, 44.93% (M), and 63.80%, 62.96%, 39.61% (MNPK), respectively. The enrichment factors of organic carbon (EC) and total nitrogen (EN) were similar in the macroaggregates and microaggregates, generally higher than those in silt and clay fractions. Both the M and MNPK treatments significantly increased the C/N ratios of water-stable aggregates, and the silt and clay fractions (except for > 2 mm aggregates). The OC sequestrated in the > 2 mm aggregates was driven by the proportions of > 2 mm, whereas, the OC sequestrated in the other water-stable aggregates, and the silt and clay fractions was driven by the OC contents. The crop yields increased linearly as the increase of OC contents in the water-stable aggregates, and the silt and clay fractions, indicating that the SOC pool in this area has not saturated, especially for the < 0.053 mm fraction. Therefore, the application of organic manure combined with NPK (MNPK) to the reclaimed soil with low fertility can be an effective way to improve soil performance in coal mining subsidence areas.