<p>Membrane bioreactors (MBRs) have been widely used in the field of wastewater treatment because of their small footprint and high treatment efficiency. In this research, 10 rural wastewater treatment sites in China that employ the MBR process were systematically studied. Specifically, treatment of actual domestic wastewater using MBRs was examined by high-throughput 16S rRNA gene sequencing to explore the microbial community composition and perform function prediction. The data of water quality parameters revealed high removal rates of chemical oxygen demand and NH₄⁺–N in all the sites. Proteobacteria were absolutely dominant in all the sites. <i>Thauera</i>, <i>Nitrospira</i>, <i>Ferribacterium</i>, and <i>Dechloromonas</i> were the main functional genera responsible for nitrogen and phosphorus removal at the tested sites. <i>Nitrospira</i> includes conventional nitrite-oxidizing bacteria and complete ammonia-oxidizing bacteria. Among them, 26 genes related to nitrogen metabolism were retrieved according to gene prediction, which verified the good NH₄⁺–N removal efficiency at the tested sites. This study focuses on the analysis of microbial community structure and functional characteristics of MBR-based treatment systems for rural wastewater treatment, thereby providing a microbial basis for improving rural wastewater treatment processes.</p> Graphical abstract <p></p>