The hybrid membrane bioreactor introduces suspended biofilm carriers into the membrane bioreactor (MBR). The microbial diversity and content with the functions of carbon reduction, nitrogen removal and phosphorus accumulation were analyzed under the optimal conditions respectively to investigate the reasons and the mechanism for the differences in decontamination efficiency between HMBR and MBR through high-throughput sequencing and related analysis software. Results showed that HMBR had better pollution removal performance than MBR, and the pollutant degradation mechanisms of MBR and HMBR were different. HMBR had more active microbial communities, which were with richer species, more evenly distributed, and larger quantities. And at the same time, relevant functional bacteria were more obviously presented in HMBR, especially the addition of suspended filler brought extra increment of functional bacteria, which promoted HMBR with better pollution removal performance.