Abstract:[Objective] This study was to explore the effect of biochar-based fertilizer application on the microbiological mechanism of the quality of tobacco-planting yellow soil. [Methods] In 2016, 3 different treatments were designed:no fertilizer (NF), conventional fertilizer (CF) and biochar-based fertilizer (BF). Illumina miseq sequencing was applied to analyze soil bacterial and fungal communities. [Results] Compared with NF and CF treatments, the yield of flue-cured tobacco was increased, the contents of soil alkaline hydrolyzed N and available P were increased significantly in the BF treatment. In the BF treatment, the number of operational taxonomic units (OTUs, 1592), abundance and diversity indexes of soil bacterial community were the highest. However, the number of OTUs (280), abundance and diversity indexes of soil fungal community were the lowest. The relative abundance of Bacteroidetes (1.50%) was increased in the BF treatment, whereas Latescibacteria (0.11%) was decreased. There were significant differences in the relative abundance of Bacteroidetes and Latescibacteria between BF and NF treatments. In addition, BF significantly decreased the relative abundance of Zygomycota (2.18%). Compared with the NF treatment, the relative abundance of Chytridiomycota (0.01%) was significantly decreased in the BF treatment. BF changed the fungal community at the genus level and significantly decreased the relative abundance of Fusarium (5.83%). Compared with the NF treatment, the relative abundance of Mortierella (2.11%), Stachybotrys (0.90%) and Alternaria (0.01%), was decreased significantly in the BF treatment. The most important soil factor causing the change of bacterial community structure was pH, and the most important soil factor causing the change of fungal community structure was available P. [Conclusion] Biochar-based fertilizers cause changes in soil biochemical environment, lead to changes in community structure, diversity of soil bacteria and fungi and then optimize soil ecology.