Background and Aims <p>Organic amendments rich in fulvic acid (FA) offer a way to improve the water and salt distribution in saline-alkali soils and enhance soil quality. As soil humus promotes the formation of soil aggregates and improves soil quality, exploring the effects of FA on saline-alkali soil aggregates and humification is significant to understand the potential of fulvic acid in improving soil quality.</p> Methods <p>This study examines severely saline-alkali cotton fields in Xinjiang through a two-year field experiment (2021–2022) using five FA application rates (0, 150, 300, 450, and 600 kg·ha⁻¹) and evaluates their effects on soil structure and humus fractions through structural equation modeling (SEM).</p> Results <p>FA application increased soil moisture by 6.16–18.64% and decreased salt content and pH by 4.07–20.87% and 0.57–1.90%, respectively, compared to standard fertilization. The application of FA improved soil aggregate stability, with optimization positively correlated to the amount applied. The soil humus components rose by 5.24–60.49%, and humification improved by 6.97–20.08%. Among them, the 600 kg·ha⁻¹ application rate yielded the most significant effects Additionally, SEM revealed that soil physical and chemical properties (path coefficient = 0.436, <i>p</i> &lt; 0.001) and humus components (path coefficient = 0.442, <i>p</i> &lt; 0.001) in saline-alkali cotton fields had a direct positive impact on soil humification. Additionally, soil aggregates indirectly enhanced humification by influencing humus content and soil properties.</p> Conclusion <p>FA-mediated stabilization of soil aggregates, along with salt inhibition and improved soil moisture retention, enhances saline-alkali soil structure and accelerates humification. Therefore, the results provide technical and theoretical support for reducing nutrient loss and promoting sustainable management of saline-alkali soils.</p>