[Objective] Lycium ruthenicum Murr. is an important medicinal and halophyte plant of Solanaceae family in desert regions of China. Our study aims to reveal the diversity and distribution of endophytic bacterial community in different tissues of Lycium ruthenicum Murr.. [Methods] Through high-throughput sequencing technology, sequences at V5-V7 regions of endophytic bacteria 16S rRNA gene in different tissues of Lycium ruthenicum Murr. were amplified, and community composition, diversity and function were analyzed by bioinformatics. [Results] The diversity and function of endophytic bacterial community in different tissues of Lycium ruthenicum Murr. were significantly different. The OTUs (operational taxonomic units) of flower, leaf, fruit, stem and root were 182, 173, 119, 187 and 254, respectively. The community diversity index showed that root > flower > fruit, stem > leaf. At the level of phylum, Proteobacteria was the dominant group, which was simultaneously found in different tissues. The relative abundances of flower, leaf, fruit, stem and root were 87.66%, 41.51%, 81.76%, 97.67% and 61.85%, respectively. At genus level, the distribution of endophytic bacteria displayed difference in different tissues. Serratia and Acinetobacter were the dominant groups in flower, with relative abundances of 11.57% and 8.55%, respectively. Rhodococcus and Bradyrhizobium were the dominant groups in leaf, with relative abundances of 29.68% and 5.53%, respectively. Pantoea，Rhodococcus and Serratia were the dominant groups in fruit, with relative abundances of 23.12%, 5.52% and 4.29%, respectively. Serratia and Pseudomonas were the dominant groups in stem, with relative abundances of 12.03% and 17.71%, respectively. Halomonas, Fodinicurvata and Lipingzhangella were the dominant groups in roots, with relative abundances of 24.18%, 5.16% and 4.86%, respectively. Some dominant microbial groups, such as Halomonas, Serratia, Acinetobacter, Rhodococcus, Pantoea etc., exhibited functional characteristics related to salt tolerance, promoting growth, biological control, degradation of toxic and harmful substances and anti-oxidation etc. PICRUSt function prediction analysis showed that the functions of endophytic bacteria in different tissues were involved in the biosynthesis of secondary metabolites such as polysaccharides, terpenes, ketones, enzymes and vitamins etc. [Conclusion] The endophytic bacteria of Lycium ruthenicum Murr. had rich community and functional diversity. They also contained a variety of probiotics and functional information related to human and plant metabolism. The dominant bacteria genera and functional information of different tissues were different, among which the endophytic bacteria species in the root were the most abundant, and the bacteria involved in various metabolic functions in the flower and stem were the highest. In addition, there were a large number of unknown species and genera in tissues, which provided a broad development space to explore functional utilization of endophytic bacteria and find new microbial resources.