Abstract: To investigate the relationship between the occurrence of tobacco hollow stalk and the diversity of environmental bacteria, high-throughput sequencing (Illumina MiSeq) technology was employed to compare and analyze differences in bacterial community structure and diversity in the stems and leaves of healthy and Dickeya chrysanthemi-infected plants. After inoculation with the hollow stalk pathogen Dickeya chrysanthemi strain NPEc1, the Shannon index and Simpson index of endophytic bacteria in tobacco leaves decreased, while the OTU number, Chao1 index, and Faith-PD index of endophytic bacteria in both diseased stems and leaves increased significantly. The dominant phyla in stems and leaves were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, among which the abundance of Bacteroidetes increased significantly in diseased leaves. At the genus level, Cupriavidus was the dominant genus in both healthy and diseased stem and leaf tissues. In diseased leaves, the abundances of Cupriavidus and Dickeya increased significantly, while the abundance of Halomonas decreased significantly. In diseased stems, the abundance of Dickeya increased significantly, while the abundance of Burkholderia decreased significantly. Seven metabolic pathways, including (5R)-carbapenem carboxylate biosynthesis (PWY-5737) and polymyxin resistance (PWY0-1388), exhibited significant differences between healthy and diseased stem tissues; among these pathways, Dickeya had the highest abundance and the greatest contribution. These results indicate that infection of tobacco by the hollow stalk pathogen can alter the bacterial community structure in stems and leaves, leading to microecological imbalance, disrupting plant metabolic pathways, and ultimately aggravating disease occurrence.