Purpose <p>Soil salinization may cause substantial soil quality deterioration, leading to decreased crop production, especially in coastal regions. Despite this, the effects of amelioration on soil quality via soil structure and hydraulic functions remain unclear.</p> Materials and methods <p>Herein, we characterized the alterations in soil aggregation, cementing agents involved, and pore structure identified by X-ray CT from a 7-year trial in Yellow River Delta, North China. Three treatments were included: no ameliorant (CK), manure compost only (MC), and manure compost combined with flue gas desulfurization gypsum (MC + FG), and samples were taken from both 0–20&#xa0;cm and 20–40&#xa0;cm layers.</p> Results and discussion <p>The results showed that applied MC alone and especially combined with gypsum (MC + FG) markedly enhanced soil macroaggregates by 1.95–7.64 times and mean weight diameter by 0.93–2.55 times in comparison to CK in topsoil. This improvement was likely attributed to the increased organic cementing agents (e.g., soil organic C, permanganate-oxidizable C, and extracellular polymeric substances) and ions such as Ca²⁺ and Mg²⁺. Organic and Ca ameliorants (MC and MC + FG) enhanced 3D pore structure in topsoil, showing higher image-identified porosity by 2.6–2.8 times, and pore connectivity by 1.9–2.7 times, along with the optimized pore-size distribution (e.g., 100–500, and &gt; 500&#xa0;μm). The enhanced 3D pore features observed in the reclaimed saline soils could potentially boost water holding capacity by 20.7–31.0% and saturated hydraulic conductivity by 88.3-205.9% in the upper soil treated.</p> Conclusion <p>Collectively, either manure compost alone or in combination with Ca-based ameliorants boosts overall soil physical quality and soil quality by 50.4–155.0%, offering effective solutions for rehabilitating saline soil.</p>