In order to explore the effects of increasing application of organic fertilizer on organic carbon and nitrogen components and microbial community in saline-alkali soil, the wheat-maize rotation sample plot in the saline-alkali reclamation area of the Yellow River Delta since 2018 was taken as the research object. The content of soil organic carbon and nitrogen components and the response of microbial community to the measures of increasing organic fertilizer under three treatments (common chemical fertilizer CN, chemical fertilizer plus pig manure organic fertilizer PCOF, and no fertilizer CK) were measured, aiming at providing a theoretical basis for the improvement of organic fertilizer and the sustainable development of agriculture in the saline-alkali land of the Yellow River Delta. The results showed that: (1) The input of fertilizer played a positive role in promoting saline-alkali soil. Compared with the application of chemical fertilizer alone, the content of basic nutrients such as nitrogen, phosphorus and potassium in soil increased significantly by 15.6%, 251.7% and 65.2% respectively (p＜0.05). Moreover, the plough layer structure has been improved. (2) Combined application of inorganic and organic fertilizers was helpful to increase the active components of soil organic carbon and nitrogen. Compared with CN, POC, DOC and MBC were significantly increased by 40.8%, 13.2% and 69.1% respectively. HTN and AAN increased significantly by 11.6% and 33.3% respectively. Compared with CK, EOC and MBC of single application of chemical fertilizer significantly increased by 32.9% and 17.5% respectively, and organic nitrogen components had no significant effect. (3) After three years of combined application of organic fertilizer, the diversity of bacterial community and the richness of fungal community were significantly higher than that of CK and CN, and the relative abundance of beneficial bacteria such as Acidobacteria, Curvularia and Ascomycetes increased. (4) RDA analysis showed that organic carbon and organic nitrogen components had a significant positive correlation with the relative abundance of beneficial bacteria in microbial community, and a significant negative correlation with the relative abundance of Oligotrophic Bacteria. In conclusion, increasing the application of organic fertilizer is an effective measure to improve the organic carbon and nitrogen components of saline-alkali soil, as well as the diversity of bacterial community and the richness of fungal community.