<p>Organic amendments show potential for improving soil structure in coastal salt-affected soils, yet the relative contributions of abiotic and biotic factors to aggregate formation and stability remain unclear. In this study, we evaluated relative contribution of physicochemical and microbial determinants in governing soil aggregate formation and stability in coastal salt-affected soils amended with sewage sludge (S) and sludge-based vermicompost (V) at 0, 50, and 100 t ha^− 1. Results indicated that aggregate improvement depended strongly on the carbon source and application rate, with the most pronounced effects observed under S100 and V50 treatments. Organic reclamation not only mitigated saline-alkali stress and nutrient deficiency but also drove a reassembly of the bacteriome with distinctive core and unique community profiles. Redundancy analysis linked bacteriome restructuring to modified microhabitat conditions in the amended soils, such as pH, salinity, soil organic carbon (SOC), aggregation status, and microbial activity. Procrustes analysis confirmed a strong coupling between soil aggregation and the integrated soil physicochemical properties and the bacteriome. Furthermore, an integrated analysis combining redundancy analysis, random forest, and structural equation modeling collectively demonstrated that aggregate formation and stabilization were governed by synergy of determinants, primarily SOC, followed successively by the C/N ratio, pH, total microbial activity, community diversity, and specific bacterial core taxa such as <i>Micrococcaceae</i> and <i>Hyphomicrobiaceae</i>. Overall, this study preliminarily elucidates the relative contributions of abiotic and biotic factors to soil aggregation in coastal saline‑alkali soils. It reveals that amendment carbon quality governs synergistic effects in which abiotic constraint alleviation enables bacteriome reassembly, jointly enhancing aggregation. This insight establishes a crucial basis for precise soil management in coastal reclamation.</p>