Soda salinization changes the characteristics and function of farmland soil and is one of the key factors that threaten crop growth and soil quality. At present, there have been relatively limited studies on the effect of adding organic composts as soil amendments on the enzyme activity, microbial community structure, and microbial interactions in different layers of saline-alkali soils. In this study, we explored the application of organic composts made from cow manure to 0-10cm, 10-20cm, 20-30cm soil catalase, alkaline phosphatase, urease, dehydrogenase, cellulase, and soil bacteria community structure changes. After applying organic composts, catalase, alkaline phosphatase, urease, dehydrogenase, and cellulase at a depth of 0-10 cm increased by 21.11%, 205.22%, 48.81%, 83.17%, 18.26%, respectively, compared with unapplied soil. Meanwhile, the growth rate of enzyme activity in the soil decreased with the increase of depth, except for catalase and cellulase. The six main bacterial phyla were detected in all soil samples, including Actinobacteriota, Proteobacteria, Chloroflexi, Gemmatimonadota, Acidobacteriota, and Firmicutes (accounting for more than 82.99% of the reads). The soil which applied composts increased the bacterial community diversity and bacterial richness in three different depths. Phylogenetic molecular ecological network (pMEN) analysis further showed that the addition of organic composts led to changes in the bacterial community structure and bacterial interactions, and enhanced the stability of the bacterial community structure in saline-alkali soils. In conclusion, the continuous application of organic composts for 7 years had a positive effect on the improvement of the enzyme activity of saline-alkali soil, and it could improve the application method of saline-alkali soil based on improving the stability of the bacterial community.