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Soils constitute one of the most critical natural resources and maintaining their health is vital for agricultural development and ecological sustainability. Driven by excessive fertilizer application and frequent irrigation, soil degradation has become a global issue that seriously threatens the soil original functions and food security. In such degraded soils, severe nutrient imbalances directly restrict plant growth and carbon inputs. Additionally, weakened soil structure exposes formerly protected organic carbon to microbial decomposition, accelerating carbon loss and threatening agricultural sustainability. Chitin-rich organic amendments, owing to their rich nutrient contents and unique structures, offer promising potential for maintain or increase SOC sequestration and enhancing soil fertility in degraded soils. However, their potential effects on soil properties, soil microbial community structure, as well as soil structure and the underlying mechanism of carbon sequestration are poorly understood. Therefore, we conducted a series of field, greenhouse, and incubation experiments in sandy and salt-affected soils. In sandy soil, we evaluated the effects of chitin-rich organic amendments on microbial community diversity, structure, and function using 16S rRNA and ITS amplicon sequencing combined with metagenomic analysis to elucidate the microbial mechanisms of carbon stabilization. In salt-affected soil, greenhouse and incubation experiment were performed to investigate their impacts on organic carbon fractions, soil aggregate formation, pore structure, microbial community structure and network, thereby revealing both structural and microbial pathways of SOC sequestration. The main research results are as follows: (1) Microorganisms have different responses to different soil amendments. Bacteria dominated the microbial community and were strongly influenced by chitin-rich organic amendments. 14 OTUs belonging to five phyla (Proteobacteria, Actinobacteriota, Firmicutes, Gemmatimonadota, and Patescibacteria) related to the decomposition of organic matter were enriched in chitin-rich organic amendment application, while 22 OTUs belonging to six phyla (Proteobacteria, Actinobacteriota, Firmicutes, Gemmatimonadota, Patescibacteria, and Cyanobacteria) were enriched significantly in co-application of chitin-rich organic amendment and inorganic amendment, suggesting enhanced microbial functional capacity. The metagenomic analysis showed that amendment-induced changes in pH, AP, enzyme activity, SOC, and microbial structure jointly influenced carbon metabolism and SOC stabilization potential. (2) Chitin-rich organic amendment significantly increases soil electrical conductivity (EC), salt ion content and labile SOC fractions in both soil layers; while reduces pH in topsoil. The bio-organic amendment notably increased the proportion of large macroaggregates and aggregate stability in both layers. In contrast, the chitin-rich organic amendment specifically enhanced small macroaggregates in the topsoil and large macroaggregates in the subsoil (P<0.05). Redundancy analysis identified soil pH as a crucial factor influencing topsoil aggregation, while EC, Mg2+, and Ca2+ were critical for subsoil aggregation. Organic amendments increased SOC, with higher Ca2+ and Mg2+ levels under lower pH in the topsoil improving aggregate stability. In the subsoil, elevated EC, primarily driven by increased Ca2+ and Mg2+ (excluding Na+), facilitated aggregate formation and accumulation of recalcitrant organic carbon, thereby contributing to SOC stabilization. (3) Chitin-rich organic amendment resulted in greater pore structure and microbial communities. The total porosity, connected porosity, meso- (30–75 µm) and macroporosity (75–500 and >500 µm), pore throats numbers, equivalent throat radius and channel length significantly increased in amendment-induced soil, indicating that chitin-rich organic amendment exhibited a complex and denser pore structure. The structure of microbial community was significantly altered following chitin-rich organic amendment, and these changes were certainly related to the soil pore structure. In addition, organic amendment enhanced the cumulative C mineralization, and structural equation modelling indicated that chemical properties induced by organic amendment changed SOC mineralization through dual pathways: directly by restructuring pore structure (including porosity and pore-throat network characteristics) and indirectly by mediating bacterial keystone taxa. In conclusion, chitin-rich organic amendments can improve degraded soil quality and enhance SOC sequestration through structural and microbial processes. The findings provide theoretical and practical support for sustainable soil management and carbon sequestration in degraded agricultural ecosystems.