Abstract: The present study is aimed at improving the efficiency of vertical flow artificial wetlands in the purification of rural domestic wastewater, constructing a bio-rotary-coupled vertical flow constructed wetland system, and revealing the relationship between the structure of the microbial community and the pollutant treatment efficacy. Actual domestic wastewater is used as the research object in order to study the purification effects of bio-rotary-coupled vertical flow wetland construction and the microbial community structure, as analyzed by high-throughput sequencing. The results show that the removal rates of chemical oxygen demand (COD), ammonium-ion nitrogen content (NH₄⁺-N), and total phosphorus (TP) were 64.97%, 86.84% and 79.18%, respectively, with the average concentrations of 71.70, 3.21, and 0.67 mg·L^–1, respectively, in the effluent. These results demonstrate that the proposed wetland system is suitable for treating domestic wastewater with COD, NH₄⁺-N and TP concentrations of < 250, 30-50 and < 2 mg·L^-1, respectively, and 24 h is the optimal operating time of the system; There were no significant differences in microorganism species in each filling area (volcanic stone and zeolite) of the bio-rotary-coupled vertical flow system and the conventional treatment system, while the relative abundances varied greatly. Each system contains 5, 8, and 10 categories of dominant phylum, class, and order, respectively, with little differences in species. In particular, the nitrogen removing microorganisms in the new system are mainly Hydrogenophaga and Pseudomonas, while the phosphorus-removing microorganisms are mainly Pseudomonas, Dechloromonas, Acinetobacter, and Rhodococcus. Notably, the NH₄⁺-N, TP, and COD removal are positively correlated with the presence of Proteobacteria and Cyanobacteria, while the TP concentration is positively correlated with Chloroflexi, and the COD is positively correlated with Chlorobi(P < 0.05), and each pollutant is mainly removed in the volcanic stone and zeolite areas. The present results clarify the structural characteristics of the microbial community in the bio-rotary coupled vertical flow constructed wetland and its relationship with pollutant removal, thus providing a scientific reference for further improving the treatment efficiency of the artificial wetland.