Microorganisms perform a crucial function in the biogeochemical processes that maintain soil quality. Nonetheless, the influence of biochar on soil microbial communities and their ecological functions remains poorly understood in black soils. To investigate this, a 2-year field experiment was conducted with four biochar application treatments: 0 t ha− 1 (CK), 6 t ha− 1 (BC6), 12 t ha− 1 (BC12), and 24 t ha− 1 (BC24). Microbial diversity and community composition under each treatment were assessed using high-throughput sequencing techniques. PICRUSt2 and FUNGuild were employed to predict microbial functional profiles. Compared to the control (CK), biochar addition led to notable shifts in both bacterial and fungal community structures. It also significantly enhanced bacterial α-diversity, as reflected by increased Shannon index, OTU counts, and Chao1 richness. However, a gradual decline in bacterial diversity was observed with rising biochar application rates. Taxonomic analysis revealed that biochar treatment significantly elevated the relative abundances of specific bacterial groups—such as Acidobacteria, Chloroflexi, Candidatus_Solibacter, and Bryobacter—as well as fungal groups such as Ascomycota, Zygomycota, Mortierella, Penicillium, and Fusarium. These effects were most evident under the moderate application rate (BC6). These microbial community changes may contribute to maintaining agroecological functions and soil health in biochar-amended soils. Regarding ecological functions, biochar application enhanced soil bacterial metabolic potential and saprotrophic fungal abundance, with more significant effects in the BC6 treatment, while reducing plant pathogenic fungi. This suggests beneficial effects on soil health maintenance and elemental cycling. Therefore, from the perspective of soil microbial community characteristics, biochar application positively influences black soil quality improvement. Considering environmental and economic benefits, a lower biochar application rate (6 t ha⁻1) may represent an optimal strategy for carbon sequestration, soil quality enhancement, and agroecological function maintenance in the studied system.