Despite increasing interest in sustainable soil management, the mechanisms by which long-term green manure and straw return impact Fe-organic associations and soil organic carbon (SOC) stabilization in paddy soils are unclear. This study examines their effects on SOC stability, aggregate fractionation, Fe oxides, aggregate stability, and SOC composition in macro- and micro-aggregates. A well-established 8 year field experiment with four treatments, i.e., Chinese milk vetch without straw incorporation and fertilizer (CK), winter fallow without straw incorporation and with NPK (WF+NSR+NPK), winter fallow with straw incorporation and NPK (WF+SR+NPK), and Chinese milk vetch with straw incorporation and with NPK (MV+SR+NPK), were selected. The results demonstrated that the MV+SR+NPK treatment significantly (p < 0.05) increased SOC storage in macroaggregates by 18.2 % compared to CK, while reducing SOC in microaggregates and non-aggregated fractions by 1.14 % and 21.54 %, respectively. Additionally, this treatment enhanced soil aggregation, as evidenced by a 26.33 % increase in mean weight diameter (MWD) and a 54.62 % increase in geometric mean diameter (GMD), alongside a 21.5 % rise in macroaggregate formation. Further, SOC stability was reinforced by a 16.8 % increase in aromatic-C content and a 19.4 % rise in the aromatic-C/aliphatic-C ratio depicting enhanced chemical stability and resistance to degradation. Amorphous (Feo) and complex Fe oxides (Fep) in macroaggregates were 13.5 % and 17.9 % higher than in CK. In comparison, the WF+SR+NPK treatment improved MWD by 25.94 %, GMD by 31.93 %, and SOC in macroaggregates by 1.69 %, with significant increases in Feo and Fep contents by 39.92 % and 102.08 %, respectively. Furthermore, the aromatic-C/aliphatic-C ratio increased by 33.9 %, indicating enhanced SOC stability. Conversely, the WF+NSR+NPK treatment decreased MWD by 12.97 %, with only a slight increase in SOC and Fed in finer aggregates by 0.80 % and 3.12 %, respectively. These results demonstrate that the co-utilization of green manure and straw return, in combination with NPK fertilization, significantly (p < 0.05) enhances SOC stabilization and aggregate stability by promoting Fe-organic associations, thereby contributing to long-term carbon sequestration in paddy soils.