Abstract: In order to analyze the existence pattern and growth-promoting mechanism of the growth-promoting bacteria with different IAA secretion characteristics in plants, Lysinibacillus xylanilyticus CZ29, the plant growth-promoting bacteria that could not produce IAA, and Rhizobium radiobacter GF12, the plant growth-promoting bacteria that could produce IAA, were used as the materials to be inoculated in the roots of potted tomato seedlings, Xinzhongshu No.4, and the high-throughput sequencing based on the variable region of the bacteria 16S rRNA gene V5-V7 was used to analyze the colonization of the two different growth-promoting bacteria in plant roots whose growth has been promoted and their effect on the structure and diversity of endophytic bacterial flora in plant roots. The results showed that after inoculating the two growth-promoting bacteria, the colonization of the two growth-promoting bacteria in the plant roots whose growth has been promoted did not change significantly, indicating that the growth-promoting effect of the growth-promoting bacteria inoculation was not achieved by increasing the colonization of the inoculated strains. After the inoculation with two different growth-promoting bacteria respectively, there was no significant difference (P>0.05) between the species richness (Chao1 index) and bacterial diversity (Shannon index) of endophytes in tomato roots compared to the control group and between each other, which showed that the growth-promoting effect of these two growth-promoting bacteria was not directly related to the richness and diversity of endophyte flora. The analysis of hierarchical clustering based on OTU level and PLS-DA showed that the inoculation of the two growth-promoting bacteria could significantly affect the composition of the endophyte flora in tomato root, causing the balance of the original endophytic flora to be broken but the specific effects were different. Among them, the probiotics such as Roseateles, Sphingobium and Rhizobium were significantly enriched in the group inoculated with L.xylanilyticus CZ29, the plant growth-promoting bacteria that could not produce IAA; the harmful bacteria such as Myroides, Chryseobacterium, Achromobacter and Strenotrophomonas were significantly inhibited (P<0.05). In the other experimental group inoculated with R.radiobacter GF12, the plant growth-promoting bacteria that could produce IAA, the average abundance of each bacterial genus did not fluctuate significantly compared with the control group, and the microbial community structure was more similar to that of the control group and showed a more stable structure. Therefore, it was hypothesized that L.xylanilyticus CZ29, the plant growth-promoting bacteria that could not produce IAA, promoted the plant growth by inhibiting the harmful bacteria through the enrichment of probiotics, while Rhizobium radiobacter GF12, the plant growth-promoting bacteria that could produce IAA, promoted the plant growth by simultaneously up-regulating the abundance of the main flora of plant endophytes to construct a more stable endophytic flora, thus to increase the anti-irritating ability of plants and secrete IAA.