High salinity, poor soil structure and nutrient deficiencies are the main limitations in saline-alkali soils. We investigated the effects on the microstructure, and the aerobic and anaerobic bacterial communities in the macroaggregates following addition of vermicompost and humic acid fertilizer to saline-alkali soil. These effects could enhance salt leaching and inhibit nitrogen losses in the topsoil. Vermicompost and humic acid fertilizer improved soil aggregate stability and the microstructure of macroaggregates (porosity, path tortuosity and effective porosity), which in turn increased soil permeability and salt leaching in saline-alkali topsoil. The improvement in aggregate microstructure affected the soil bacterial community of the macroaggregates by increasing the relative abundances of aerobic heterotrophs, such as Chloroflexi and Bacteroidetes. Additionally, vermicompost and humic acid fertilizer influenced nitrogen cycling by the macroaggregate microbial community, and stimulated nitrification by increasing archaeal and bacterial amoA gene copy numbers in the topsoil, but inhibited nitrite-reducing bacteria by decreasing nirS and nirK gene copy numbers. Furthermore, these amendments increased microbial N2O reduction by increasing nosZ gene copy numbers, suggesting that vermicompost and humic acid fertilizer have the potential to reduce N2O emissions in saline-alkali soil. In summary, vermicompost and humic acid fertilizer can ameliorate saline-alkali soils by replenishing organic matter, improving aggregate microstructure, and regulating the microbial community, which could increase salt leaching and inhibit nitrogen losses. •Vermicompost (V) and humic acid fertilizer (H) improved aggregate microstructure in saline soil.•Improvement in aggregate microstructure affected soil bacterial community in macroaggregates.•Improvement in aggregate microstructure increased salt leaching and inhibited nitrogen loss.•V and H ameliorated saline soil by increasing SOM and improving aggregate microstructure.