In this study, the three biofilm-anoxic-oxic-MBR systems were operated in parallel using different carbon source feed types. The three systems were operated with complete sludge retention to compare microbial community composition and system efficiency. High average removal of ammonia and COD was obtained in the three reactors. However, total nitrogen and total phosphorus removal efficiency were significantly higher in the VFAs feed systems when compared with the glucose feed system. The highest and most stable BNR efficiency was observed when acetate was used as a carbon source. The qPCR analysis revealed that ammonium oxidizing bacteria, denitrifiers and total bacteria were all highest in the acetate feed system followed by the propionate feed system. Moreover, among all carbon source types, the PUS-biofilm could maintain a higher degree of abundance of total bacteria than the sludge biomass. Meanwhile, ammonium oxidizing bacteria and denitrifiers were enriched in the sludge biomass rather than in the PUS-biofilm. The results of illumina sequencing revealed that acetate followed by propionate were favourable to the growth of microorganisms that were associated with the BNR process, which was the main reason for the high efficiency of nutrient removal in the acetate and propionate feed systems.