Activated sludge contains highly complex microbial communities, which play crucial roles in pollutant removal performance in wastewater treatment plants (WWTPs). Metagenomic sequencing was applied to characterize microbial community and functional profiles within activated sludge from a full-scale municipal WWTP carrying out simultaneous nitrogen and phosphorous removal (SNPR). We applied the assembled contigs (N90 of 591 bp) and predicted genes to conduct taxonomic and function annotations, respectively. Results revealed the extraordinary microbial diversity of activated sludge, which included detection of minority populations that are difficult to be explored by traditional molecular methods. Taxonomic analysis indicated that the dominant bacterial phyla were Proteobacteria, Nitrospirae, Bacteroidetes, Actinobacteria and Firmicutes. The abundance of the key organisms involved in nitrogen and phosphorous removal were qualified. Aerobic ammonia-oxidizing bacteria distinctly dominate over ammonia-oxidizing archaea and anaerobic ammonium oxidation bacteria. Various key enzymes involved in the global nitrogen cycle were annotated in the activated sludge. High abundance of the known polyphosphate accumulating organisms was detected (approximately 4.89% of the overall population reads), supporting good phosphorous removal performance. This study provides a comprehensive insight into the community structure and diversity of the SNPR system, and will provide foundation for optimal operation of nutrient removal systems.