Quinazoline derivatives have wide biological activities and therapeutic properties, implying their potential for development and application on a large scale. In the present study, 2-(4-chlorophenyl)-4-(4-methoxyphenyl) quinazoline (CMQ), was selected to examine its effect on unicellular cyanobacteria, Microcystis aeruginosa by evaluating growth, physiological and molecular responses. Growth was inhibited by CMQ, with a 96 h EC50 of 1.93 ± 0.19 mg L−1. The up-regulated expression of prx was shown, reflecting that oxidative stress might be a toxic factor of CMQ. At higher concentrations of CMQ, the quantum yields of Y(II) and Y(NPQ) in photosystem II decreased seriously and Y(NO) increased sharply, and psbA gene encoding for D1 protein was over-expressed. These results demonstrated that high concentrations of CMQ had different inhibitory targets associated with photosystem electron transport and with sites beyond the electron transport chain, leading to severe toxicity.