Abstract: Three groups of sequencing batch reactors (SBRs) were operated to investigate the long-term effects of multi-walled carbon nanotubes (MWCNTs) on activated sludge systems. Each group was set up in triplicate. The long-term effects of 1 and 20 m/L MWCNTs on nutrient removal of activated sludge process were investigated. In addition, bacterial community structure in activated sludge was studied using MiSeq high-throughput sequencing. It was found that 20 mg/L MWCNTs adversely affected the performance of biological nitrogen removal, which significantly reduced the average TN removal efficiencies from 83.4% to 71.7%, and average TN removal efficiencies from 83.7% to 79.7%, after long-term exposure to 1 mg/L MWCNTs. In addition, both 1 and 20 mg/L MWCNTs inhibited biological phosphorus removal, with the average TP removal efficiencies decreasing from 98.0% to 52.0% and from 98.2% to 34.0%, respectively. MiSeq sequencing indicated that 1 and 20 mg/L MWCNTs obviously decreased the diversity of bacterial community in activated sludge. MWCNTs differentially enhanced the abundance of α-Proteobacteria and γ-Proteobacteria, and reduced the abundance of Bacteroidetes. The long-term effects of 1 mg/L MWCNTs significantly enhanced the abundance of glycogen accumulating organisms (GAOs) (i.e. Defluviicoccus and Micropruina), which are thought to out-compete the polyphosphate-accumulating organisms (PAOs) in activated sludge communities removing phosphate. The long-term effects of 20 mg/L MWCNTs significantly decreased the abundance of 16 core genera.