Abstract: To explore the effect of microbial agent on the endophytic bacterial community structure of Alpinia oblongifolia, the seedlings of A. oblongifolia were used as test materials, a mixture of Enterobacter aerogenes, Bacillus amyloliquefaciens and Acinetobacter calcoaceticus was administered by injecting the root. The roots and tubers of A. oblongifolia were collected at the 3rd and 6th month after application. The samples were measured using 16S rRNA high-throughput sequencing. The findings revealed that at the phylum classification level of endophytic bacteria in A. oblongifolia, the dominant bacterial phyla were all Proteobacteria. At the genus level, the dominant bacterial genera changed after microbial agent administration. Before using microbial agents, the dominant bacterial genera are Burkholderia, Pseudomonas, Corynebacterium, Cloacibacterium, Allorhizobium, Bradyrhizobium, Amycolatopsis, Mycobacterium, Herbaspirillum. In the 3rd month after application, Burkholderia, Pseudomonas, Corynebacterium, Pipebacterium and Dyella were the dominant bacterial genera. At the 6th month after application, Burkholderia, Pseudomonas, Corynebacterium, Pipebacterium and Heterorhizobia were the dominant bacterial genera. The correlation network analysis of endophytic bacterial groups showed that the correlation network structure changed from loose to a tighter chain in the 3rd month after the application of microbial agent, and the number of core bacterial genera decreased. A relationship network was formed with Burkholderia, Pseudomonas, Corynebacterium and Cloacibacterium as core endophyte genera. At the 6th month after the application of microbial agent, the network structure among the core endophyte genera was closer, and the connections between each genus were more compact. The application of microbial agent can affect the composition of the endophytic bacterial community of A. oblongifolia, enhance the abundance of endophytic functional microorganisms, and improve the ability of A. oblongifolia to absorb soil nutrients.