In order to explore a novel and potential method using carbon nanotubes (CNTs) for controlling blue-green algal blooms efficiently in future, effects of single-walled carbon nanotubes (SWCNTs) on Microcystis aeruginosa growth control were investigated under lab cultured conditions. Related physiological changes were tested involving several important enzyme of antioxidant defense system (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), malondiadehyde (MDA), photosynthetic pigments, protein, soluble sugar and extracellular microcystin toxins (MC-LR)). Algal cell density was significantly inhibited by SWCNTs at high concentration (>5.00 mg/L), and the inhibition rate was dose-dependent. For treatment with 100 mg/L SWCNTs, the inhibitory rates even reached above 90%. 96 h IC50 was determined as 22 mg/L. Antioxidant enzyme activities were dramatically dropped with increasing lipid peroxidation at higher SWCNTs concentration, indicating intracellular generation of reactive oxygen species (ROS) and oxidative stress damage in algae. Reduction of photosynthetic pigments, soluble sugar and protein contents suggested that SWCNTs may severely ruin algal photosynthesis system, destroy the metabolism-related structure of cell, and thus lead to negative physiological status in M. aeruginosa. Besides, SWCNTs can effectively decrease the amount of extracellular microcystins in culture medium.