Residues of triazophos in aquatic ecosystems due to extensive use for controlling pests in agriculture has became worldwide concern, while the toxic response of triazophos on the non-target green algae in aquatic environment is not well studied. Therefore, the acute (96 h) toxic effects of 1 and 10 mg/L triazophos on green algae Chlorella pyrenoidosa were evaluated in present study. The results showed that the growth was notably inhibited when treated with triazophos and the 96 h-EC50 (median inhibition concentration) were 12.79 mg/L. The content of photosynthetic pigments (including chl a, chl b, total-chl and carotinoids) clearly decreased under two treatments after 48 h and 96 h with exception for the values at 48 h exposure in 1 mg/L treatment. In addition, the transcript abundance of photosynthesis-related genes (psbA, psbC and rbcL) showed obvious decrease in above two treatments after exposure 96 h to triazophos. In response to 10 mg/L triazophos treatment, the morphology of thylakoid chloroplast of algal cells were obviously damaged. It was also found that starch granules increased with down-regulation of atpB gene expression in 10 mg/L treatment, which suggests that triazophos may inhibit the energy metabolism of C. pyrenoidosa. Moreover, the algal growth inhibition was along with the increase of intracellular reactive oxygen species (ROS), activity of antioxidant enzymes and malondialdehyde content indicating oxidative damage and lipid peroxidation in the algal cells. Our findings reveal that triazophos has potential toxicity and environmental risks to one of the primary producers green algae.