Deciphering the various types of interactions between plants and their microbiomes is a hot topic for research in ecology as well as in plant sciences and agronomy. To analyse and compare the differences in microbial communities in different compartments of Chinese chives, high-throughput sequencing technology was employed to amplify and sequence the V5-V6 region of the 16S rDNA of microorganisms in the leaves, phylloplanes, stems, roots and rhizospheres of Chinese chives. The sequences were clustered by operational taxonomic units (OTUs), and the community composition of bacteria between the endosphere (inner tissues) and ectosphere (outer surfaces) of Chinese chives was analysed based on the OTU. Overall, the results indicated that the endophytic bacteria in Chinese chives mainly include Proteobacteria, Actinobacteria, and Actinomycetes. Alpha diversity index analysis and OTU number analysis showed that the bacterial diversity and richness of the underground plant compartments were higher than those of the above-ground parts. PCoA based on the OTU level showed that the vertical stratification structure of plants and compartments had significant effects on the bacterial community structure. The richness of endophytic bacteria also varied greatly among the different varieties of Chinese chive. A considerable number of endophytic bacteria form symbiotic and mutually beneficial relationships with host plants, which play an important role in regulating host growth, metabolism and stress resistance. Further investigations are needed to uncover the evolution of interactions between plants and endophytes.