Barren paddy fields characterized by poor soil structure, shallow tillage layers and low organic carbon content are a common limitation to rice production in subtropical China. As a novel approach to soil improvement, granulated organic amendments offer significant potential. Previous studies have shown that granulated straw can improve soil physicochemical properties and rapidly increase the soil organic carbon (SOC) content. However, their effects on barren paddies remain underexplored. This study evaluated four soil amendment strategies: no organic amendments (CK), 10 t ha^–1 of composted manure (M10), 20 t ha^–1 of granulated organic amendment (G20), and 40 t ha^–1 of granulated organic amendment (G40). The objective was to assess the effects of these amendments on soil structure, the contents of aggregate-associated carbon (AAC), particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and the chemical stability of MAOC among various size aggregates in both topsoil (0–20 cm) and subsoil (20–40 cm). The results demonstrated that organic amendment inputs significantly increased the macroaggregate (>250 µm) proportion and improved soil structural stability. These amendments also elevated the carbon concentration within aggregates of various sizes and facilitated the redistribution of organic carbon from microaggregates (53–250 µm) and silt+clay fractions (<53 µm) to macroaggregates. The proportion of POC to AAC declined with decreasing aggregate size, whereas the proportion of MAOC increased. In the topsoil, macroaggregate formation enhanced the protection of POC, supported the accumulation of non-hydrolyzable carbon within MAOC, and accelerated the formation of intra-microaggregates. In the subsoil, mineral-bound organic carbon remained the dominant form of carbon sequestration. In conclusion, the application of 40 t ha^–1 of granulated organic amendment proved to be a successful tactic for enhancing soil physicochemical structure, increasing SOC content, and improving carbon stability. This approach offers a promising and innovative solution for the sustainable management and restoration of barren paddy fields.