Biochar can affect soil microbial abundance and community structure due to its excellent physiochemical properties. Our previous study of soil bacterial community discovered that the relative abundance of Acidobacteria was significantly influenced by biochar. In this study, we further investigated the effect of biochar on acidobacterial community composition generated with Acidobacteria-specific primers ACIDO/342 R using Illumina MiSeq sequencing in the same black soil samples after 3 years of biochar application. The qPCR results showed that biochar addition increased the acidobacterial abundance, especially at the rates of 4% and 8%. There were 18 acidobacterial subgroups detected, and Gp4 and Gp6 were the most abundant subgroups. The relative abundance of Gp4 was positively correlated with soil total potassium and negatively correlated with soil pH, while Gp6 was on the opposite. Biochar addition did not influence the alpha-diversity but altered the acidobacterial community composition. Redundancy analysis revealed that changes in the soil acidobacterial community compositions were closely associated with soil properties, such as pH, total potassium and available potassium. Given that these soil properties were highly correlated with biochar addition, which suggested that the long-term impacts of biochar on the soil acidobacterial community were indirectly driven by changes in soil properties.