The toxicity of cetyltrimethylammonium bromide (CTAB) on the growth and biochemical indicators of algae was studied by taking Chlorella pyrenoidosa as the test organism. The results showed that 96 h EC50 of CTAB on Chlorella pyrenoidosa was 0.17 mg/L; algal chlorophyll, protein content and Superoxide Dismutase (SOD) activity first increased and then decreased, the content of algal chlorophyll and activity of SOD rose slightly in low concentrations of CTAB (≤0.06 mg/L) and decreased dramatically in a higher concentration(＞0.06 mg/L); when the dosage of CTAB≤0.24 mg/L, the protein content increased, however it decreased obviously with a higher addition of CTAB (≥0.30 mg/L); lipid peroxidation malondialdehyde (MDA) content rose gradually with the increase of CTAB concentrations. According to 5 kinds of active parameter variation rules and the measured results of algal cell apoptosis by flow cytometric apparatus, it was speculated that CTAB first destroyed the integrity of the cell membrane, thereby inhibited the SOD activity, leading to the MDA content rising continually. Therefore, the restrained SOD activity leading to peroxidation of the membrane lipid may be the main reason CTAB causes toxicity on Chlorella pyrenoidosa.