The low-methane transgenic rice is an ideal rice material for low-carbon production of rice. The production of methane is driven by microorganisms in paddy soil. Changes in soil microbial community composition of low methane emission transgenic rice not only affect paddy field methane emission, but also affect the stability of soil microbiological system. In this study, the differences of microbial communities and the abundance of functional genes in paddy soil with between low-methane transgenic rice (86R27-3) and wild-type rice (MH86) were analyzed by high-throughput sequencing of 16S rRNA gene or ITS gene and fluorescence quantitative PCR of functional genes, such as mcrA、nifH、amoA and nirS. The results showed that there were no differences in α-diversity of bacterial communities in paddy soil with between 86R27-3 and MH86, and the α-diversity of Shannon, Simpson and Pielou_e index of fungal communities in paddy soil with 86R27-3 were higher than those of MH86 only under the tillering stage of rice. The differences in the community composition of bacteria or fungi in paddy soil with between 86R27-3 and MH86 were also not obvious based on the analysis of β-diversity of microbial communities. However, under the heading stage of rice, the relative abundance of Actinobacteria or Rozellomycota in paddy soil of 86R27-3 was significantly higher (P ＜ 0.05) than that of MH86, and the relative abundance of Acidibacteria or Ascomycota in paddy soil of 86R27-3 was significantly lower (P ＜ 0.05) than that of MH86. The functional prediction of soil microbial community showed that the abundance of bacterial functional groups for soil metabolism of nitrogen, sulfur or manganese in 86R27-3 was significantly lower than that of MH86 (P ＜ 0.05), such as nitrate reduction, nitrate respiration, thiosulfate and sulfur respiration under the tillering stage of rice, aerobic nitrite oxidation under the heading and maturation stages of rice or manganese oxidation at maturation stage of rice. Compared with MH86, there were decrease and increase in the abundance of soil fungal functional groups of 86R27-3, such as the abundance of its Undefined Saprotroph of Tremellales, Pseudeurotium, Fusarium and Westerdykella significantly decreased (P ＜ 0.05) under different growth periods of rice, while the abundance of its Animal Endosymbiont-Undefined Saprotroph of Pichia and Undefined Saprotrophthe of Lasiosphaeriaceae significantly increased (P ＜ 0.05) under tiller stage of rice (P ＜ 0.05). Quantitative PCR analysis of microbial functional genes showed that the abundance of methanogenic bacterial mcrA gene in paddy soil of 86R27-3 was significantly lower (P ＜ 0.05) than that of MH86; and the abundance of nitrogen-fixing bacterial nifH gene, ammonia-oxidizing bacterial amoA gene and denitrifying bacterial nirS gene were also significantly reduced (P ＜ 0.05) in paddy soil of 86R27-3. In conclusion, low-methane emission transgenic rice (86R27-3) had no significant impact on the composition of soil bacteria or fungal communities, but could change the relative abundance of major species of bacteria or fungi and the abundance of some bacterial or fungal functional groups, and significantly reduce the abundance of microbial functional genes in paddy soil.