Sustainable agricultural management practices improve soil processes, prevent soil erosion and consequently enhance crop productivity. The integrated agricultural practice (IP) developed in northeast China, by altering row spacing of planting, adopting no-tillage and returning all crop residues, showed great benefit in sustaining crop yield. However, its effect on the soil microbiome remains largely elusive. This study evaluated the effect of 12-year integrated agricultural practice on the structure and activity of the soil microbial community at different soil depths in China's Mollisols zone. The experiment consisted of integrated agricultural practice and conventional practice (CP) treatments in a split-plot arrangement. The soil microbial community was characterized by MiSeq sequencing. The results showed that agricultural practices affected 12 phyla, 24 classes, 32 orders and 75 families in the bacterial community and one phyla, four classes, 12 orders and 18 families in the fungal community. Integrated agricultural practice resulted in greater bacterial richness and diversity, and increased the relative abundances of Actinobacteria, Gemmatimonadetes, Verrucomicrobia and Ascomycota, but reduced Bacteroidetes, Firmicutes and Basidiomycota in the dominant bacterial and fungal phyla. These findings suggested that integrated agricultural practice modified the soil physiochemical properties and consequently altered microbial community structure and diversity, which in turn affected soil microbial biomass and enzyme activities. These changes under integrated agricultural practice could have contributed to the enhanced crop yield, suggesting that IP is a sustainable agricultural practice. Highlights: How does soil microbial community change in the IP and CP soils? IP affected the soil microbial community and activity. Bacterial and fungal community structure correlated significantly with soil physiochemical properties. IP is a promising sustainable agricultural practice.