Activated sludge system is an important process of domestic and industrial wastewater treatment containing highly diverse microbial communities. In this study, high-throughput sequencing was applied to examine the microbial community composition and diversity of activated sludge samples from four full-scale municipal wastewater treatment plants (WWTPs) in Shanghai. A relationship between microbial communities and environmental variables was examined. Proteobacteria was the most dominant phylogenetic group, followed by Bacteroidetes and Firmicutes. A total of 166 genera were commonly shared by all seven sludge samples, including Zoogloea, Dechloromonas, Thauera, Nitrospira, Arcobacter, etc. Besides these shared populations, certain unique bacterial populations were found abundant in individual sludge sample. Canonical correspondence analysis (CCA) indicated that influent COD and pH had the greatest influence on microbial community compositions, whereas dissolved oxygen (DO) exhibited the least influence. The operating process was likely to foster diversity of the microbial communities inhabiting the wastewater treatment facilities. Alternative operation methods including a fluctuation of anoxic, oxic, and anaerobic conditions were favorable for promoting the growth of diverse microbial populations in activated sludge systems.