[Objective] The purpose of this research is to study the effects of herbicide "starane" on the structure and diversity of bacterial communities in different micro-environments. [Methods] We used the high-throughput sequencing technique Illumina Miseq to determine the V4-V5 variable region sequence of 16S rRNA in endophytic, rhizosphere and non-rhizosphere soils of maize roots. The herbicides were sprayed in different growth stages, and we researched the herbicide effect on the structure and diversity of maize root endophytes as well as soil bacteria. [Results] We obtained a total of 544393 effective sequences and 333565 high-quality sequences from 15 samples. The multi-sample OTU analysis showed that the community structure of non-rhizosphere soil and rhizosphere soil was similar, which indicated that the colonization of maize-related bacteria was selective and the gradual specialization from rhizosphere to root. The results of rank abundance curve and Alpha diversity showed that the richness and uniformity of non-rhizosphere and rhizosphere soil were higher, while the richness and uniformity of endophytic community in maize roots of mature stage were lower. The abundance of endophytic community in maize roots was significantly reduced by the application of herbicides. The composition analysis of the community showed that the distribution of bacteria in the maize roots was with a great change at both the Phylum and Genus level. The prediction of metabolic function of the flora indicated that the growth pressure of the microorganisms was gradually increased from the seeding stage to the mature stage of the corn, which required more energy for bacterial metabolism and environmental adaptation. [Conclusion] The application of herbicide "starane" can reduce the diversity of bacterial community in the roots of maize, and the effect on the endophytic community of maize roots is more obvious.