Noni fruit is rich in bioactive components with strong antagonistic and antioxidant activities. This study was carried out to explore the difference of endophytic bacterial diversity in Hainan noni fruit and the connection between their key activities and diversity. The common dominant bacterial genera from 4 varieties of noni fruit (long fruit labeled L, round fruit labeled R, conjoined fruit labeled C, and Tahitian fruit labeled T) was identified by high-throughput sequencing technology as Brevundimonas, Pantoea and Bacillus. The antagonistic activity of endophytic bacteria was tested, then the total antioxidant activity of the endophytic bacteria with antagonistic activity was further determined. It was found that there was antioxidant activities among all the endophytic bacteria with antibacterial activity, and the antioxidant values were found to be in the range of 3.07-20.78U·mL-1, and the antioxidant activities of the endophytic bacteria were positively correlated with antagonistic activities. Eight endophytic strains from 4 varieties of noni fruit with strong activities were selected for 16S rDNA and gyrA molecular identification. The endophytic bacteria were identified as Bacillus and belonged to Bacillus subtilis, Bacillus mojavensis and Bacillus pumilus, respectively. The results of this study compared the diversity differences of endophytic bacteria communities in different varieties of noni fruit from the perspective of microbiology, and explored the correlation between the function of endophytic bacteria and endophytic community, confirming the theory of plant-microbial interactions. It was hoped that this study could provide help for the future research on the coordination and unity of endophytic bacteria and their host functions, provide a theoretical basis for the screening and application of endophytic bacteria with specific functions in noni fruit, and provide more ideas for the application of endophytic bacteria in the food industry and the research on the interaction between plants and microorganisms.