This study aimed to investigate the impact of the replanting of basswood Ganoderma lingzhi on the soil bacterial community and reveal the obstacle phenomenon of replanting basswood G. lingzhi. In this study, the soil bacterial community of wild 20 cm (N0a) and 40 cm deep soil (N0b), cultivated once (N1a, N1b) and twice (N2a, N2b), were investigated by Illumina MiSeq sequencing. The predominant bacterial phyla at the phylum classification level were Acidobacteria, Chloracidobacteria, Nitrospira, Spartobacteria, Gemmatimonadetes, Acidobacteria-6. Still, only the relative abundance of Chloracidobacteria and Acidobacteriia increased after two years of replanting of basswood G. lingzhi. At the genus level, the dominant genus included many unclassified bacteria. Among the known genera, the best genus was DA101, which showed a decreasing trend after two years of replanting. Network analysis showed that more connections of bacterial communities were observed in soil samples of the group "a," indicating that the replanting of basswood G. lingzhi can affect the relationship between soil bacterial communities at depths. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis showed that the gene metabolism function of soil bacteria was quite different after one year of replanting basswood G. lingzhi. The replanting of basswood G. lingzhi changed the composition and function of the soil bacterial community, and also affected the bacterial community diversity in the soil at different depths.