In order to explore the improvement effects of the combined application of biological and chemical methods on saline-alkali soil in the Yellow River Delta, we first modified fly ash and isolated indigenous salt-tolerant bacteria, and then selected two strains of salt tolerant bacteria (BY-4 and BY-8) to carry out an indoor soil column leaching experiment in combination with a chemical compound amendment (i.e., modified fly ash+desulfurization gypsum+humic acid (FSZ)). The changes of base cations, dissolved organic carbon (DOC), sodium adsorption ratio (SAR) and soil organic matter in leachate and/or soil were studied. The results showed that the two strains BY-4 and BY-8 were salt tolerant and had the abilities to produce indole acetic acid and to solubilize phosphate or potassium. In compared with the treatment (CK), treatments with chemical compound amendments (FSZ) significantly promote the leaching of water-soluble Na⁺, reduced the total amount of water-soluble Na⁺ and SAR in soil, and increased the contents of DOC and organic matter in soil. The treatment of BY-8 combined with chemical compound amendment (FSZ8) performed the best. Compared with CK, soil total water-soluble Na⁺ under FSZ8 treatment decreased by 33.30%, SAR of arable soil decreased by 79.76%, DOC leaching loss decreased by 34.60% and organic matter content of arable soil increased by 79.47%. These findings were helpful to understand the role of salt-tolerant bacteria in soil improvement, and would provide theoretical and data reference for the development and utilization of biological and chemical composite amendments in the future.