Abstract: By taking 46 endophytic bacteria isolated from tomato plants as the research objects, the endophytic bacteria from tomato roots were used to infect the tomato seeds to study the effects on tomato plant growth. Then, the phylogenetic trees were further constructed by using the sequences of the 16S rDNA combined with the previously open OTU (Operational Taxonomic Unit) sequence of tomato root to analyze the species and abundance of major growth-promoting endophytic bacteria. The results of the experiment showed that the tested endophytic bacteria could promote the fresh weight of tomato plants. Bacillus (3 strains), Pseudomonas (2 strains), Xanthomonas (1 strain) and Rhizobium(2 strains) could significantly promoted the fresh weight of tomato plants (P < 0.05), while compared with the control group, GF12 has promoted the fresh weight most significantly (P < 0.01), and the increase of endophytic bacteria of GF12 on the fresh weight of tomato plants was 1.69 times that of the control group. There were 9 endophytic strains with significant promotion of the plant height, including Bacillus (5 strains), Pseudomonas (2 strains), Xanthomonas (1 strain) and Rhizobium (1 strain). CZ29 significantly promoted the plant height and elongation compared with the control group (P < 0.01), and the tomato plant height after the infection of CZ29 was 1.46 times that of the control group. In addition, the tested 8 endophytic bacteria promoted the elongation of tomato roots, among which the tomato root length after the infection of MR56, GF12 and CZ29 was more than 15% longer than that of the control group. The phylogenetic analysis of the 16S rDNA sequence of 46 endophytic bacteria and the first 100 core OTU sequences of endophytic bacteria in tomato roots showed that the tested endophytic bacteria were clustered into Pseudomonadales, Enterobacteriales, Rhizobiales, Burkholderiales, Bacillales, Flavobacteriales and Xanthomanadales. In addition, the endophytic bacteria clustered into Pseudomonas and Rhizobium were clustered together with OTU_3 (Pseudomonas) and OTU_23 (Rhizobium) with high abundance in tomato roots, indicating that Pseudomonas and Rhizobium were the core microorganisms for the main growth promoting effect in tomato roots. There were the most types of probiotic Bacillus isolated which had the effect of promoting growth, but Pseudomonas and Rhizobium were abundant in roots, which were the most important groups in the endophytic microbiome of healthy tomato roots. Therefore, Bacillus, Pseudomonas and Rhizobium had great potential to promote growth, which could be used as biological fertilizer to provide nutrition for the host, and rationally develop and utilize microbial resources to better develop the agriculture.