Carriers strengthened duckweed treatment system (CDW), duckweed treatment system (DW) and water hyacinth treatment system (WH) were developed to treat rural wastewater in Dianchi Lake basin. Results showed that adding microbial carrier did not affect the growth and biomass components of duckweed. The following features were discovered in the CDW system. First, the NO3--N and TN removal efficiencies were the highest among three systems, reaching 80.02% and 56.42%, respectively. Secondly, Illumina sequencing revealed the highest microbial diversity. Thirdly, a distinct succession of microbial community was observed. Rhodobacter, Bacteria vadinCA02, C39 and Flavobacterium dominated in the start- up stage, and contributed to biofilm formation and pollutants degradation. Acinetobacter, Planctomyces and Methylibium significantly increased in the stable stage, and contributed to nitrogen removal. Finally, highly abundant plant growth- promoting bacteria were found. Comprehensive analysis indicated that the functional bacteria community was closely related to the pollutant removals, plant growth and system operating status.