Bacillus thuringiensis is an effective entomopathogen, and its crystal toxin expressed in transgenic crops has been widely used for pest control. However, insect resistance risk is the main threat to the continued successful utility of Bt crops. Several studies reported the role of midgut microbiota in Bt resistance, but the mechanism remains controversial. In the present study, using high-throughput sequencing of the bacterial 16S ribosomal RNA gene, we surveyed the midgut bacterial flora of Ostrinia furnacalis from one Bt-susceptible (ACB-BtS) and two Bt-resistant (ACB-AbR and ACB-FR) strains and explored the mortality of O. furnacalis after eliminating the gut bacteria. Gut bacterial diversity in Bt-resistant strains was significantly lower in Bt-resistant than in Bt-susceptible strains. Ordination analyses and statistical tests showed that the bacterial community of ACB-AbR was distinguishable from ACB-BtS. The genus Halomonas was dominated in ACB-BtS, but the unclassified_Enterobacteriaceae was the most enriched genus in ACB-AbR and ACB-FR. Furthermore, interactions of the bacterial community are more complex in Bt-resistant strains than in Bt-susceptible strains. Moreover, the mortalities of ACB-AbR and ACB-BtS strains treated by the Cry1Ab toxin were significantly reduced after eliminating the gut bacteria. Our findings suggest that Bt stressors structured in the midgut bacterial community and the microbiota have the potential to regulate the Bt-induced killing mechanism.