Severe eutrophication and harmful cyanobacterial blooms of freshwater ecosystems has been a persistent environmental topic in recent decades. Allelochemical inhibition has received great attention in aquatic ecology and quality management. This study investigates the growth and full photosynthesis performance of pyrogallol on Microcystis aeruginosa TY001. The growth and pigment contents of M. aeruginosa were seriously inhibited by pyrogallol. The relative expression levels of the nblA gene were up-regulated under pyrogallol treatments. Unexpectedly, the relative transcript abundance of the psaB and psbA genes significantly increased compared with the control, but the chlorophyll fluorescence parameters of M. aeruginosa TY001 decreased significantly, except at 1 mg L^-1 pyrogallol. In conclusion, the target sites of pyrogallol’s toxic effect on the PSII of M. aeruginosa TY001 were mainly on the active reaction centers and the electron transport at the acceptor side.