Salt-affected soils frequently experience leaching and desalination issues, which severely restrict plant growth and water uptake. Hence, in this experiment, four treatments including CG (no amendments addition); OF (organic fertilizer addition); OH (organic fertilizer and Hekang amendment addition); and OB (organic fertilizer and fulvic acid addition) were designed to examine the effect of organic amendment on soil chemical properties, water and salt transport, and soil desalination laws of coastal saline soil. The results showed that the addition of organic amendments significantly reduced soil pH (8.47–8.52) and salt content (2.06–2.34 g kg−1), while increasing soil organic matter content, available phosphorus, and available potassium. OH treatment has a higher available phosphorus content than other treatments. OH and OB treatments elevated the soil desalination ratio (32.95% and 32.12%, respectively) by raising the leaching volume and leaching rate. Organic amendments significantly promoted Na+ (4.5–32%) and SO42− (12–27%) leaching compared to CG. Organic treatments, particularly OB treatment, not only increased the content of soil organic matter and available nutrients but also promoted salt ion leaching, improved soil permeability and increased soil desalination and water leaching rates. Our results may provide a theoretical basis for revealing the desalination law of coastal saline soil.