Field experiments have shown that the mixed anaerobic digestion of straw with livestock and poultry manure can improve the efficiency of biogas production. We hypothesize that inoculation with livestock and poultry manure increase the efficiency of methane production by improving the diversity and structure of microbial community in the field anaerobic digestion system. In this study, an experimental system was established to simulate the microbial community of the mixed anaerobic digestion system in the field. The methane production and taxonomic composition of bacterial and archaeal communities in the rice straw anaerobic digestion systems were determined. We aim to reveal the effects of the inocula on the diversity and composition of bacterial and archaeal communities and the mechanism underlying the impact on biogas production in the field. The following results were obtained. (1) Inoculation significantly improved the efficiency of methane production in anaerobic digestion, and the best performance was achieved with treatment A (cleared biogas slurry), which obtained methane production that were 39.59 %, 106.85 %, and 123.00 % higher than in treatment B (pig manure extract), C (cleared biogas slurry + pig manure extract), and the control, respectively. (2) The inocula increased the abundance and diversity of bacterial communities in the early and middle stages and archaeal communities in the early stage. (3) The inocula also had a significant impact on bacterial and archaeal community composition in the early and middle stages. The inocula increased the relative abundance of Aquamicrobium_A, Proteiniphilum, and Cryptobacteroides but reduced the relative abundance of Macellibacteroides, Acinetobacter, and Phocaeicola. The dominant genus of archaeal community was altered from Methanosarcina to Methanocorpusculum. (4) It is concluded that inoculation significantly increase methane production as the inocula improve the abundance and diversity of bacteria and archaea of anaerobic digestion systems in the early and middle stages of digestion, as well as improve the structure and metabolic pathway of archaeal communities.