Soil microbial community diversity and composition are responsive to biochar application. However, the impacts of biochar application on soil microbial community structure and interactions in different aggregate fractions are poorly understood. We conducted a 3-year field trial involving biochar application to black soil in northeastern China. Four biochar treatments were applied: 0 (B0, control), 10 (B10), 30 (B30) and 50 (B50) t ha⁻¹ biochar. Compared to the B0 treatment, biochar application significantly decreased the diversity of bacterial and fungal communities. In addition, biochar application significantly increased the relative abundances (RAs) of Bacteroidetes and Proteobacteria and significantly decreased those of Actinobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia. Moreover, the B30 and B50 treatments significantly increased and decreased the RA of Nitrospirae, respectively. Moreover, the RA trends of Acidobacteria, Nitrospirae and Planctomycetes among different aggregate fractions was mega-aggregates (ME; > 2 mm) > macroaggregates (MA; 0.25–2 mm) > microaggregates (MI; < 0.25 mm); the RAs of Basidiomycota and Glomeromycota in ME were higher than those in MA and MI. The RA of Ascomycota in MI was the highest among the different aggregate fractions. The co-occurrence networks showed that the B30 treatment enhanced microbial interactions in terms of the number of links, average degree, and modularity, while the B50 treatment reduced these interactions. Additionally, co-inertia analysis demonstrated that the microbial interactions in ME were enhanced by biochar application. Thus, an appropriate biochar application (e.g., 30 t ha⁻¹ used in the present study area) can enhance soil microbial interactions, especially in ME.