Abstract: The modified alternative process was used as the research object in two sewage treatment plants in Suzhou. According to different control strategies, the process model was used to analyze the operation characteristics of the process. At the same time, high-throughput sequencing technology was used to analyze the composition of the microbial community, aiming to provide a reference for the operation of the modified alternating process in sewage treatment. Based on the OTU(Operational Taxonomic Unit) data, the dominant bacteria in the two plants were the same at the phylum level, but the abundance was different. The relative abundances of Actinobacteria and Chloroflexi in the LJ plant were higher than those in the FX plant, which led to a better biological phosphorus removal effect in the LJ plant than in the FX plant. Genus-level species composition, the genera with relatively high relative abundance mainly included Caldilineaceae, Saprospiraceae and Trichococcus, whose relative abundances can reach 3.62%～5.57%, 2.85%～5.03%,0.01%～6.47%, respectively. Combined with the RAD(Representational difference analysis) analysis results, the model simulation method was used to analyze the influence of HRT(Hydraulic Retention Time) and DO on the operation effect of the two plants. The main reason that the phosphorus removal effect of the LJ plant was better than that of the FX plant may be its shorter HRT.