Abstract: In order to understand the effect of transgenic Bacillus thuringensis (Bt) cotton on rhizosphere soil microbial community, based on field experiments, high-throughput sequencing technology was used to study the composition and diversity of transgenic and non-transgenic cotton rhizosphere soil microbial community at different growth stages (pre-sowing, seedling and boll-opening stages). The results showed that the dominant phylum in rhizosphere soil of transgenic cotton and its parents were Proteobacteria (0.4338-0.4993), Bacteroidetes (0.1060-0.1366), Actinobacteria (0.0749-0.1464), Gemmatimonades (0.0542-0.0723), Acidobacteria (0.0538-0.0899). The relative abundance of dominant phylum in rhizosphere soil was significantly affected by transgenic cotton at different growth stages (P < 0.05). There were no significant differences in Shannon-Wiener, Simpson, Sobs and PD indices between transgenic cotton and its parents at different growth stages (P>0.05), but PCoA analysis showed that the soil microbial communities of transgenic cotton and its parents had spatial differences at seedling and boll opening stages (P < 0.05). The Bt protein content in rhizosphere soil of transgenic cotton was significantly different at different growth stages, and the Bt protein content in rhizosphere soil of transgenic cotton was significantly higher than that of its parents at seedling stage and boll opening stage. The Bt protein content of rhizosphere soil was significantly related to the relative abundance of bacterial phylum level. The Bt protein in rhizosphere soil of transgenic cotton was significantly correlated with the relative abundance of dominant phylum (P < 0.05). The Bt protein in the rhizosphere of transgenic cotton at different growth stages affected the relative abundance and community structure of soil bacteria, but did not affect alpha diversity.