Abstract: Microorganisms drive the soil material cycle and evolution of fertility, and their community composition is related to the stability and sustainability of the soil microecosystem. The study of changes in the soil microbial community in insect-resistant transgenic rice is an important part of environmental safety assessments. Based on high-throughput sequencing of the bacterial 16S rRNA and fungal ITS genes, this study analyzed the differences in diversity and composition of microbial communities in paddy soils with insect-resistant transgenic rice ‘MFB’, insect-resistant transgenic hybrid rice ‘Minfeng A/MFB’ ‘Tianfeng A/MFB’ or ‘Gufeng A/MFB’ and non-transgenic conventional rice ‘Minhui 3301’ or hybrid rice ‘Tianyouhuazhan’. The results showed that, compared with non-transgenic conventional rice ‘Minhui 3301’ or hybrid rice ‘Tianyouhuazhan’, both insect-resistant transgenic rice ‘MFB’ and transgenic hybrid rice ‘Minfeng A/MFB’ ‘Tianfeng A/MFB’ or ‘Gufeng A/MFB’ could significantly increase the yield (P<0.05). At the same time, high-throughput sequencing showed that the α-diversity indexes of Chao1, Observed_species, and Shannon of bacterial or fungal communities in paddy soil with ‘MFB’ were higher than those in soil with ‘Minhui 3301’ at all stage except for fungal communities at rice maturation stage, and the differences at rice maturation or tillering stage are significant (P<0.05). At the heading stage of rice, the values of α-diversity indexes of Shannon of bacterial or fungal communities in paddy soils with the insect-resistant transgenic hybrid rice ‘Minfeng A/MFB’ ‘Tianfeng A/MFB’ or ‘Gufeng A/MFB’ were between those of soils with ‘MFB’ and ‘Tianyouhuazhan’. The results of β-diversity analysis of bacterial or fungal communities showed that there were no significant differences in the composition of microbial communities in paddy soils with different varieties of rice in this field experiment. However, the relative abundance of Proteobacteria, which showed the highest abundance of bacteria, in paddy soil with ‘MFB’ increased compared with that of ‘Minhui 3301’, and reached the significance level at the tillering and maturation stage of rice (P<0.05). In contrast, the relative abundance of Ascomycota, which showed the highest abundance of fungi, was reduced in paddy soil with ‘MFB’ and reached the significance level at the tillering and heading stages of rice (P<0.05). At the heading stage of rice, the relative abundances of Proteobacteria and Ascomycota in paddy soils with ‘Minfeng A/MFB’ ‘Tianfeng A/MFB’ or ‘Gufeng A/MFB’ were between those of soils with ‘MFB’ and ‘Tianyouhuazhan’. According to the functional prediction of microbial communities, the differences in functional composition of bacterial communities in paddy soil between soils with ‘MFB’ and ‘Minhui 3301’ gradually increased with rice growth. In summary, insect-resistant transgenic rice and its transgenic hybrid rice increased the diversity of soil bacterial and fungal communities and changed the relative abundance of major bacterial and fungal species with increased yield, but did not have significant effects on the community and functional composition of bacteria or fungi.